------------------------------------------------------------------------
r2566 | gaser | 2024-03-19 20:23:32

Changed paths:
 M CHANGES.txt
 M cat_stat_check_cov_old.m
 M cat_stat_homogeneity.m
 M cat_surf_results.m
 M cat_vol_addtruecolourimage.m
 M cat_vol_slice_overlay.m

Changed: Replaced isnan by ~isfinite which also considers Inf values in 
         cat_stat_check_cov_old.m and cat_stat_homogeneity.m.
Changed: Updated calls to cat_vol_slice_overlay.m.
Fixed:   Corrected handling of white background in cat_vol_slice_overlay.m.
------------------------------------------------------------------------
r2565 | robertdahnke | 2024-03-14 15:38:20

Changed paths:
 M CHANGES.txt
 M cat_long_main.m
 M cat_long_multi_run.m
 M cat_main_LAS.m
 M cat_main_registration.m
 M cat_main_reportfig.m

(1) Fixed:   Corrected issue in using other Templates and output resolutions
             in the longitudinal pipeline. Use default 1.5 mm in average processing
             that has to fit to the TPM in cat_long_main. Removed the warning
             for different output resolutions in cat_long_multi_run. Corrected
             definitions in cat_main_registration.   
(2) Fixed:   Corrected problem with missing text in the cat_report. 
(3) Fixed:   Corrected an bug in writing the affine/rigid background image in 
             cat_main_write.
(4) Fixed:   Corrected bug in LAS in case of some image with negative background. 
------------------------------------------------------------------------
r2564 | gaser | 2024-03-10 19:24:34

Changed paths:
 M CHANGES.txt
 M cat_vol_groupwise_ls.m
 M cat_vol_series_align.m
 M compile.m

Changed: Added try/catch to cat_vol_series_align.m because for data with strong
         anisotropy, we have to change the internal resolution for longitudinal 
         registration to "optimal".
Changed: Updated compile.m.

   ------------------------------------------------------------------------
r2560 | gaser | 2024-03-08 08:55:25

Changed paths:
 M CHANGES.txt
 M Contents.m
 M Makefile
 M cat_plot_boxplot.m
 M cat_system.m
 M cat_vol_groupwise_ls.m
 M doc/cat.html
 M doc/index.html

Fixed:   Removed search for missing binaries in cat_system because this does
         not work on Windows.
Changed: If Hessian is negativ in cat_vol_groupwise_ls.m , this issue can be
         solved by recalculating the bsplins coefficients with different border
         condition.
------------------------------------------------------------------------
r2558 | gaser | 2024-02-28 15:30:40

Changed paths:
 M CHANGES.txt
 M Contents.m
 M Makefile
 M cat_amap.mexa64
 M cat_ornlm.mexa64
 M cat_sanlm.mexa64
 M cat_surf_results.m
 M cat_vbdist.mexa64
 M cat_vol_downcut.mexa64
 M cat_vol_eidist.mexa64
 M cat_vol_genus0.mexa64
 M cat_vol_gradient3.mexa64
 M cat_vol_interp3f.mexa64
 M cat_vol_laplace3.mexa64
 M cat_vol_laplace3R.mexa64
 M cat_vol_localstat.mexa64
 M cat_vol_median3.mexa64
 M cat_vol_median3c.mexa64
 M cat_vol_pbtp.mexa64
 M cat_vol_simgrow.mexa64
 M doc/cat.html

Changed: Updated mex-files for Linux (thanks to James C. Ford)
Changed: Added Mac Intel standalone version to Makefile.
------------------------------------------------------------------------
r2557 | gaser | 2024-02-26 09:20:06

Changed paths:
 M CHANGES.txt
 M Contents.m
 M Makefile
 M cat_io_data2mat.m
 M cat_main_update_intnorm.m
 M cat_run_newcatch.m
 M cat_surf_render2.m
 M doc/cat.html

Changed: Added piwik field about Matlab version for errors.
Changed: Replaced old cg_hist2d calls by cat_plot_histogram.m.
Changed: Added ARM64 standalone to Makefile.

------------------------------------------------------------------------
r2550 | gaser | 2024-02-21 11:16:06

Changed paths:
 M CHANGES.txt
 M Contents.m
 M doc/cat.html
 M doc/index.html

Changed: Updated documentation and version information.

------------------------------------------------------------------------
r2548 | gaser | 2024-02-19 11:56:16

Changed paths:
 M CHANGES.txt
 M cat_vol_slice_overlay.m

Changed: Updated option to go to next or previous file in cat_surf_results.m.
------------------------------------------------------------------------
r2547 | gaser | 2024-02-19 11:52:37

Changed paths:
 M CHANGES.txt
 M cat_vol_slice_overlay.m

Changed: Updated option to go to next or previous file in cat_surf_results.m.
------------------------------------------------------------------------
r2546 | gaser | 2024-02-19 11:15:38

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_surf_results.m
 M doc/cat.html
 M slice_overlay.m

Changed: Added option to go to next or previous file in cat_surf_results.m.
------------------------------------------------------------------------
r2543 | robertdahnke | 2024-02-18 19:13:09

Changed paths:
 M CHANGES.txt
 M cat_io_xml2csv.m
 M cat_run.m
 M cat_surf_createCS2.m
 M cat_surf_createCS3.m
 M cat_vol_pbtsimple.m

1) Fixed:    Corrected output in cat_surf_createCS[2|3].
2) Fixed:    Setup gyrusrecons cases in cat_vol_pbtsimple using  
             the thickness phantoms. 
3) Fixed:    Corrected cell export in cat_io_xml2csv.    
4) Changed:  Optimized CSV export in cat_run.
5) New:      Internal display function cat_tst_histBWPT.        
             
------------------------------------------------------------------------
r2542 | robertdahnke | 2024-02-15 19:42:10

Changed paths:
 M CHANGES.txt
 M cat_run.m
 M cat_surf_createCS2.m
 M cat_surf_createCS3.m
 M cat_vol_pbtsimple.m

1) Fixed:    Corrected cat_surf_createCS[2|3] debugging output. 
2) Fixed:    Corrected ROI output behaviour in cat_run.
3) Changed:  Updated gyrusreconstion in cat_vol_pbtsimple. 
------------------------------------------------------------------------
r2540 | gaser | 2024-02-14 11:18:19

Changed paths:
 M CHANGES.txt
 M cat_batch_long.sh
 M cat_conf_long.m
 M doc/index.html

Changed: Save both plasticity and aging model for long. data as default.
Changed: CUpdated html doc.
------------------------------------------------------------------------
r2538 | gaser | 2024-02-13 17:37:40

Changed paths:
 M CHANGES.txt
 M cat12.m
 M cat_conf_tools.m
 M cat_stat_check_SPM.m
 M cat_stat_check_cov_old.m
D  resources/settings/MBeautyConfigurationRules.m
D  resources/settings/MBeautyConfigurationRules.xml

Changed: Added old sample homogeneity check to GUI for use with long. data.
Changed: Call old homogeneity check in cat_stat_check_SPM if long. design is found.
------------------------------------------------------------------------
r2537 | gaser | 2024-02-13 13:38:25

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_amap.mexa64
 M cat_ornlm.mexa64
 M cat_sanlm.mexa64
 M cat_stat_analyze_ROIs.m
 M cat_vbdist.mexa64
 M cat_vol_downcut.mexa64
 M cat_vol_eidist.mexa64
 M cat_vol_genus0.mexa64
 M cat_vol_gradient3.mexa64
 M cat_vol_interp3f.mexa64
 M cat_vol_laplace3.mexa64
 M cat_vol_laplace3R.mexa64
 M cat_vol_localstat.mexa64
 M cat_vol_median3.mexa64
 M cat_vol_median3c.mexa64
 M cat_vol_pbtp.mexa64
 M cat_vol_simgrow.mexa64
 M check_pipeline/analysis/surface/RPV.dat
 M check_pipeline/analysis/surface/SPM.mat
 M check_pipeline/analysis/surface/spmF_0001.dat
 M check_pipeline/analysis/surface/spmT_0002.dat
 M check_pipeline/analysis/volume/SPM.mat
 M check_pipeline/batch_surface_pipeline.m
 M check_pipeline/batch_volume_pipeline.m
 D check_pipeline/label_orig/catROI_IXI020-Guys-0700-T1.mat
 D check_pipeline/label_orig/catROI_IXI020-Guys-0700-T1.xml
 D check_pipeline/label_orig/catROI_IXI021-Guys-0703-T1.mat
 D check_pipeline/label_orig/catROI_IXI021-Guys-0703-T1.xml
 D check_pipeline/label_orig/catROI_IXI022-Guys-0701-T1.mat
 D check_pipeline/label_orig/catROI_IXI022-Guys-0701-T1.xml
 D check_pipeline/label_orig/catROI_IXI023-Guys-0699-T1.mat
 D check_pipeline/label_orig/catROI_IXI023-Guys-0699-T1.xml
 D check_pipeline/label_orig/catROI_IXI024-Guys-0705-T1.mat
 D check_pipeline/label_orig/catROI_IXI024-Guys-0705-T1.xml
 D check_pipeline/label_orig/catROI_IXI025-Guys-0852-T1.mat
 D check_pipeline/label_orig/catROI_IXI025-Guys-0852-T1.xml
 D check_pipeline/label_orig/catROI_IXI026-Guys-0696-T1.mat
 D check_pipeline/label_orig/catROI_IXI026-Guys-0696-T1.xml
 D check_pipeline/label_orig/catROI_IXI027-Guys-0710-T1.mat
 D check_pipeline/label_orig/catROI_IXI027-Guys-0710-T1.xml
 D check_pipeline/label_orig/catROI_IXI028-Guys-1038-T1.mat
 D check_pipeline/label_orig/catROI_IXI028-Guys-1038-T1.xml
 D check_pipeline/label_orig/catROI_IXI029-Guys-0829-T1.mat
 D check_pipeline/label_orig/catROI_IXI029-Guys-0829-T1.xml
 D check_pipeline/label_orig/catROI_IXI030-Guys-0708-T1.mat
 D check_pipeline/label_orig/catROI_IXI030-Guys-0708-T1.xml
 D check_pipeline/label_orig/catROI_IXI031-Guys-0797-T1.mat
 D check_pipeline/label_orig/catROI_IXI031-Guys-0797-T1.xml
 D check_pipeline/label_orig/catROI_IXI036-Guys-0736-T1.mat
 D check_pipeline/label_orig/catROI_IXI036-Guys-0736-T1.xml
 D check_pipeline/label_orig/catROI_IXI037-Guys-0704-T1.mat
 D check_pipeline/label_orig/catROI_IXI037-Guys-0704-T1.xml
 D check_pipeline/label_orig/catROI_IXI038-Guys-0729-T1.mat
 D check_pipeline/label_orig/catROI_IXI038-Guys-0729-T1.xml
 D check_pipeline/label_orig/catROI_IXI040-Guys-0724-T1.mat
 D check_pipeline/label_orig/catROI_IXI040-Guys-0724-T1.xml
 D check_pipeline/label_orig/catROIs_IXI020-Guys-0700-T1.mat
 D check_pipeline/label_orig/catROIs_IXI020-Guys-0700-T1.xml
 D check_pipeline/label_orig/catROIs_IXI021-Guys-0703-T1.mat
 D check_pipeline/label_orig/catROIs_IXI021-Guys-0703-T1.xml
 D check_pipeline/label_orig/catROIs_IXI022-Guys-0701-T1.mat
 D check_pipeline/label_orig/catROIs_IXI022-Guys-0701-T1.xml
 D check_pipeline/label_orig/catROIs_IXI023-Guys-0699-T1.mat
 D check_pipeline/label_orig/catROIs_IXI023-Guys-0699-T1.xml
 D check_pipeline/label_orig/catROIs_IXI024-Guys-0705-T1.mat
 D check_pipeline/label_orig/catROIs_IXI024-Guys-0705-T1.xml
 D check_pipeline/label_orig/catROIs_IXI025-Guys-0852-T1.mat
 D check_pipeline/label_orig/catROIs_IXI025-Guys-0852-T1.xml
 D check_pipeline/label_orig/catROIs_IXI026-Guys-0696-T1.mat
 D check_pipeline/label_orig/catROIs_IXI026-Guys-0696-T1.xml
 D check_pipeline/label_orig/catROIs_IXI027-Guys-0710-T1.mat
 D check_pipeline/label_orig/catROIs_IXI027-Guys-0710-T1.xml
 D check_pipeline/label_orig/catROIs_IXI028-Guys-1038-T1.mat
 D check_pipeline/label_orig/catROIs_IXI028-Guys-1038-T1.xml
 D check_pipeline/label_orig/catROIs_IXI029-Guys-0829-T1.mat
 D check_pipeline/label_orig/catROIs_IXI029-Guys-0829-T1.xml
 D check_pipeline/label_orig/catROIs_IXI030-Guys-0708-T1.mat
 D check_pipeline/label_orig/catROIs_IXI030-Guys-0708-T1.xml
 D check_pipeline/label_orig/catROIs_IXI031-Guys-0797-T1.mat
 D check_pipeline/label_orig/catROIs_IXI031-Guys-0797-T1.xml
 D check_pipeline/label_orig/catROIs_IXI036-Guys-0736-T1.mat
 D check_pipeline/label_orig/catROIs_IXI036-Guys-0736-T1.xml
 D check_pipeline/label_orig/catROIs_IXI037-Guys-0704-T1.mat
 D check_pipeline/label_orig/catROIs_IXI037-Guys-0704-T1.xml
 D check_pipeline/label_orig/catROIs_IXI038-Guys-0729-T1.mat
 D check_pipeline/label_orig/catROIs_IXI038-Guys-0729-T1.xml
 D check_pipeline/label_orig/catROIs_IXI040-Guys-0724-T1.mat
 D check_pipeline/label_orig/catROIs_IXI040-Guys-0724-T1.xml
 M doc/cat.html

Fixed:   Changed format of gifti saving in cat_stat_analyze_ROIs.m.
Changed: Recompiled all mex-files.

------------------------------------------------------------------------
r2536 | gaser | 2024-02-13 09:22:07

Changed paths:
 M .gitignore
 M CAT.glnx86/CAT_3dVol2Surf
 M CAT.glnx86/CAT_AddValuesToSurf
 M CAT.glnx86/CAT_AverageSurfaces
 M CAT.glnx86/CAT_BlurSurfHK
 M CAT.glnx86/CAT_Central2Pial
 M CAT.glnx86/CAT_DumpCurv
 M CAT.glnx86/CAT_DumpSurfArea
 M CAT.glnx86/CAT_DumpSurfaceRatio
 M CAT.glnx86/CAT_FixTopology
 M CAT.glnx86/CAT_FractalDimension
 M CAT.glnx86/CAT_Hausdorff
 M CAT.glnx86/CAT_Isometize
 M CAT.glnx86/CAT_MarkDefects
 M CAT.glnx86/CAT_RefineMesh
 M CAT.glnx86/CAT_ResampleSphericalSurf
 M CAT.glnx86/CAT_ResampleSphericalSurfSPH
 M CAT.glnx86/CAT_ResampleSurf
 M CAT.glnx86/CAT_SelfIntersect
 M CAT.glnx86/CAT_SeparatePolygon
 M CAT.glnx86/CAT_SmoothConvexity
 M CAT.glnx86/CAT_SulcusDepth
 M CAT.glnx86/CAT_Surf2Sphere
 M CAT.glnx86/CAT_SurfDistance
 M CAT.glnx86/CAT_VolMarchingCubes
 M CAT.glnx86/CAT_WarpSurf
 M CAT.maca64/CAT_3dVol2Surf
 M CAT.maca64/CAT_AddValuesToSurf
 M CAT.maca64/CAT_AverageSurfaces
 M CAT.maca64/CAT_BlurSurfHK
 M CAT.maca64/CAT_Central2Pial
 M CAT.maca64/CAT_DumpCurv
 M CAT.maca64/CAT_DumpSurfArea
 M CAT.maca64/CAT_DumpSurfaceRatio
 M CAT.maca64/CAT_FixTopology
 M CAT.maca64/CAT_FractalDimension
 M CAT.maca64/CAT_Hausdorff
 M CAT.maca64/CAT_Isometize
 M CAT.maca64/CAT_MarkDefects
 M CAT.maca64/CAT_RefineMesh
 M CAT.maca64/CAT_ResampleSphericalSurf
 M CAT.maca64/CAT_ResampleSphericalSurfSPH
 M CAT.maca64/CAT_ResampleSurf
 M CAT.maca64/CAT_SelfIntersect
 M CAT.maca64/CAT_SeparatePolygon
 M CAT.maca64/CAT_SmoothConvexity
 M CAT.maca64/CAT_SulcusDepth
 M CAT.maca64/CAT_Surf2Sphere
 M CAT.maca64/CAT_SurfDistance
 M CAT.maca64/CAT_VolMarchingCubes
 M CAT.maca64/CAT_VolThicknessPbt
 M CAT.maca64/CAT_WarpSurf
 M CAT.maci64/CAT_3dVol2Surf
 M CAT.maci64/CAT_AddValuesToSurf
 M CAT.maci64/CAT_AverageSurfaces
 M CAT.maci64/CAT_BlurSurfHK
 M CAT.maci64/CAT_Central2Pial
 M CAT.maci64/CAT_DumpCurv
 M CAT.maci64/CAT_DumpSurfArea
 M CAT.maci64/CAT_DumpSurfaceRatio
 M CAT.maci64/CAT_FixTopology
 M CAT.maci64/CAT_FractalDimension
 M CAT.maci64/CAT_Hausdorff
 M CAT.maci64/CAT_Isometize
 M CAT.maci64/CAT_MarkDefects
 M CAT.maci64/CAT_RefineMesh
 M CAT.maci64/CAT_ResampleSphericalSurf
 M CAT.maci64/CAT_ResampleSphericalSurfSPH
 M CAT.maci64/CAT_ResampleSurf
 M CAT.maci64/CAT_SelfIntersect
 M CAT.maci64/CAT_SeparatePolygon
 M CAT.maci64/CAT_SmoothConvexity
 M CAT.maci64/CAT_SulcusDepth
 M CAT.maci64/CAT_Surf2Sphere
 M CAT.maci64/CAT_SurfDistance
 M CAT.maci64/CAT_WarpSurf
 M CAT.w32/CAT_3dVol2Surf.exe
 M CAT.w32/CAT_AddValuesToSurf.exe
 M CAT.w32/CAT_AverageSurfaces.exe
 M CAT.w32/CAT_BlurSurfHK.exe
 M CAT.w32/CAT_Central2Pial.exe
 M CAT.w32/CAT_DumpCurv.exe
 M CAT.w32/CAT_DumpSurfArea.exe
 M CAT.w32/CAT_DumpSurfaceRatio.exe
 M CAT.w32/CAT_FixTopology.exe
 M CAT.w32/CAT_FractalDimension.exe
 M CAT.w32/CAT_Hausdorff.exe
 M CAT.w32/CAT_Isometize.exe
 M CAT.w32/CAT_MarkDefects.exe
 M CAT.w32/CAT_RefineMesh.exe
 M CAT.w32/CAT_ResampleSphericalSurf.exe
 M CAT.w32/CAT_ResampleSphericalSurfSPH.exe
 M CAT.w32/CAT_ResampleSurf.exe
 M CAT.w32/CAT_SelfIntersect.exe
 M CAT.w32/CAT_SeparatePolygon.exe
 M CAT.w32/CAT_SmoothConvexity.exe
 M CAT.w32/CAT_SulcusDepth.exe
 M CAT.w32/CAT_Surf2Sphere.exe
 M CAT.w32/CAT_SurfDistance.exe
 M CAT.w32/CAT_VolMarchingCubes.exe
 M CAT.w32/CAT_WarpSurf.exe
 M CHANGES.txt
 M Contents.m
 M Makefile
 M cat_amap.mexmaca64
 M cat_amap.mexmaci64
 M cat_amap.mexw64
 M cat_conf_tools.m
 M cat_ornlm.mexmaca64
 M cat_ornlm.mexmaci64
 M cat_ornlm.mexw64
 M cat_run.m
 M cat_sanlm.mexmaca64
 M cat_sanlm.mexmaci64
 M cat_sanlm.mexw64
 M cat_spm_preproc_write8.m
 M cat_vbdist.mexmaca64
 M cat_vbdist.mexmaci64
 M cat_vbdist.mexw64
 M cat_vol_downcut.mexmaca64
 M cat_vol_downcut.mexmaci64
 M cat_vol_downcut.mexw64
 M cat_vol_eidist.mexmaca64
 M cat_vol_eidist.mexmaci64
 M cat_vol_eidist.mexw64
 M cat_vol_genus0.mexmaca64
 M cat_vol_genus0.mexmaci64
 M cat_vol_genus0.mexw64
 M cat_vol_gradient3.mexmaca64
 M cat_vol_gradient3.mexmaci64
 M cat_vol_gradient3.mexw64
 M cat_vol_interp3f.mexmaca64
 M cat_vol_interp3f.mexmaci64
 M cat_vol_interp3f.mexw64
 M cat_vol_laplace3.mexmaca64
 M cat_vol_laplace3.mexmaci64
 M cat_vol_laplace3.mexw64
 M cat_vol_laplace3R.mexmaca64
 M cat_vol_laplace3R.mexmaci64
 M cat_vol_laplace3R.mexw64
 M cat_vol_localstat.mexmaca64
 M cat_vol_localstat.mexmaci64
 M cat_vol_localstat.mexw64
 M cat_vol_median3.mexmaca64
 M cat_vol_median3.mexmaci64
 M cat_vol_median3.mexw64
 M cat_vol_median3c.mexmaca64
 M cat_vol_median3c.mexmaci64
 M cat_vol_median3c.mexw64
 M cat_vol_pbtp.mexmaca64
 M cat_vol_pbtp.mexmaci64
 M cat_vol_pbtp.mexw64
 M cat_vol_simgrow.mexmaca64
 M cat_vol_simgrow.mexmaci64
 M cat_vol_simgrow.mexw64
 M doc/cat.html
 M doc/index.html
 M tfceMex_pthread.mexw64

Changed: Some minor changes to doc and Makefile.
------------------------------------------------------------------------
r2535 | robertdahnke | 2024-02-08 00:06:27

Changed paths:
 M CHANGES.txt
MM cat_io_xml2csv.m
 M cat_main1639.m
M  cat_main_updateSPM1639.m
MM cat_run.m
 M cat_run_job.m
 M cat_run_job1639.m
M  cat_surf_createCS2.m
 M cat_surf_createCS3.m
MM cat_vol_pbtsimple.m
AD cat_vol_pbtsimple_fine.m
M  cat_vol_set_com.m

1) New:        Added final CSV report to cat_run with changes in cat_io_xml2csv.
			   Corrected bugs in cat_run and added surface values. 
1) Changed:    Optimized command line output of cat_vol_set_com.
3) Changed:    Slight modification of the call of the surface collision correction
               in cat_surf_createCS2/3. Slight changes in cat_surf_createCS2/3 for  
               tests of the reconstructed surfaces.               
4) Changed:    Various modifications in PBTsimple (see issue #19).
5) Changed:    Small visual modification in cat_vol_set_com. 
6) Changed:    Updated alert thresholds in cat_main_updateSPM1639.
7) Changed:    Tiny correction in the APP try-catch block in cat_run_job[1639].
------------------------------------------------------------------------
r2534 | gaser | 2024-02-04 18:02:09

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_vol_defs.m
 M cat_vol_img2mip.m
 M doc/cat.html
 M doc/index.html

Fixed: Remove error in cat_vol_img2mip.m for saving function.
Fixed: Removed error in cat_vol_defs wit OR condition.
------------------------------------------------------------------------
r2532 | gaser | 2024-01-30 16:35:45

Changed paths:
 M CHANGES.txt
 M cat_surf_createCS3.m

Changed: Added new CAT_VolMarchingCubes to CS3 surface pipeline.
------------------------------------------------------------------------
r2530 | gaser | 2024-01-29 18:30:36

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_stat_homogeneity.m
 M doc/cat.html
 M doc/index.html

(1) Changed: Updated documentation for new release.
(2) Changed: Added try/catch to call of spm_run_factorial_design in
             cat_stat_homogeneity.m because sometimes window is not
             accessible.
------------------------------------------------------------------------
r2529 | dahnke | 2024-01-24 20:26:33

Changed paths:
 M CHANGES.txt
 M cat_vol_pbtsimple.m

Changed:   Updated PBTsimple to replace the sharpening effect by another concept. 
------------------------------------------------------------------------
r2528 | rdahnke | 2024-01-24 17:01:43

Changed paths:
 M CHANGES.txt
 M cat_main1639.m
 M cat_main_reportfig.m
 M cat_surf_createCS2.m
 M cat_surf_display.m
 M cat_vol_resize.m
 M cat_vol_sample.m

1) Fixed:     Corrections for T2/PD contrasts in cat_main and cat_main_gintnorm.
2) Fixed:     Corrected internal call of vol2surf.
3) Fixed:     Corrected bug in cat_vol_resize in case of minimal reduction by 
              averaging on only 2 values.
4) Fixed:     Corrected bug in cat_surf_display and cat_main_reportfig to 
              show cerebellar surfaces. 
5) Fixed:     Deactivated T1 template mapping for (cerebellar) surface 
              reconstruction due to incorrect application of the deformation
              in cat_main1639 (was already done in cat_main).
6) Changed:   Introduced cat_io_contains in cat_main_reportfig.               
7) Comment:   Extended documentation in cat_vol_sample and cat_main1639.         
8) Fixed:     Corrected bug in cerebellar reconstruction in cat_surf_createCS2.

------------------------------------------------------------------------
r2520 | gaser | 2024-01-16 10:36:41

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_stat_check_SPM.m
 M cat_vol_pbtsimple.m
 M doc/cat.html

(1) Changed: Disable WMTC in cat_vol_pbtsimple.m.
(2) Changed: Added one more try/catch to check_orthogonality in 
             cat_stat_check_SPM.m.
------------------------------------------------------------------------
r2519 | gaser | 2024-01-15 07:50:17

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_batch_spm.m
 M cat_run.m
 M cat_stat_check_SPM.m
 M doc/cat.html

(1) Changed: Check for empty dir before creating in cat_run.m.
(2) Changed: Added try/catch to check_orthogonality in cat_stat_check_SPM.m.
------------------------------------------------------------------------
r2518 | dahnke | 2024-01-11 16:47:58

Changed paths:
 M CHANGES.txt
 M cat_main_reportfig.m
 M cat_vol_pbtsimple.m

Changed:   Updated PBTsimple (see issue #19).
------------------------------------------------------------------------
r2517 | gaser | 2024-01-09 16:15:15

Changed paths:
 D CAT.glnx86/CAT_Surf2Vol
 D CAT.maca64/CAT_Surf2Vol
 D CAT.maci64/CAT_Surf2Vol
 D CAT.w32/CAT_Surf2Vol.exe
 M CHANGES.txt
 M Contents.m
 D cat_amap_new.mexmaci64
 M cat_io_xml.m
 M cat_main_gintnorm.m
 M cat_run_job1639.m
 M cat_vol_approx.m
 M cat_vol_inpaint.m
 M cat_vol_pbtsimple.m
 M cat_vol_set_com.m
 M doc/cat.html

(1) Changed: Added warning that xml-file could not be written in cat_io_xml.m.
(2) Changed: Set default approx-function to 'nn' in cat_vol_approx.
(3) Changed: Added additional check. for xml-mat file in cat_run_job1639.m.
------------------------------------------------------------------------
r2510 | gaser | 2023-12-22 12:35:54

Changed paths:
 M CAT.glnx86/CAT_3dVol2Surf
 M CAT.glnx86/CAT_AddValuesToSurf
 M CAT.glnx86/CAT_AverageSurfaces
 M CAT.glnx86/CAT_BlurSurfHK
 M CAT.glnx86/CAT_Central2Pial
 M CAT.glnx86/CAT_DeformSurf
 M CAT.glnx86/CAT_DumpCurv
 M CAT.glnx86/CAT_DumpSurfArea
 M CAT.glnx86/CAT_DumpSurfaceRatio
 M CAT.glnx86/CAT_FixTopology
 M CAT.glnx86/CAT_FractalDimension
 M CAT.glnx86/CAT_Hausdorff
 M CAT.glnx86/CAT_Isometize
 M CAT.glnx86/CAT_MarchingCubesGenus0
 M CAT.glnx86/CAT_MarkDefects
 M CAT.glnx86/CAT_RefineMesh
 M CAT.glnx86/CAT_ResampleSphericalSurf
 M CAT.glnx86/CAT_ResampleSphericalSurfSPH
 M CAT.glnx86/CAT_ResampleSurf
 M CAT.glnx86/CAT_SelfIntersect
 M CAT.glnx86/CAT_SeparatePolygon
 M CAT.glnx86/CAT_SmoothConvexity
 M CAT.glnx86/CAT_SulcusDepth
 M CAT.glnx86/CAT_Surf2Sphere
 M CAT.glnx86/CAT_Surf2Vol
 M CAT.glnx86/CAT_SurfDistance
 M CAT.glnx86/CAT_WarpSurf
 M CAT.maca64/CAT_3dVol2Surf
 M CAT.maca64/CAT_AddValuesToSurf
 M CAT.maca64/CAT_AverageSurfaces
 M CAT.maca64/CAT_BlurSurfHK
 M CAT.maca64/CAT_Central2Pial
 M CAT.maca64/CAT_DeformSurf
 M CAT.maca64/CAT_DumpCurv
 M CAT.maca64/CAT_DumpSurfArea
 M CAT.maca64/CAT_DumpSurfaceRatio
 M CAT.maca64/CAT_FixTopology
 M CAT.maca64/CAT_FractalDimension
 M CAT.maca64/CAT_Hausdorff
 M CAT.maca64/CAT_Isometize
 M CAT.maca64/CAT_MarchingCubesGenus0
 M CAT.maca64/CAT_MarkDefects
 M CAT.maca64/CAT_RefineMesh
 M CAT.maca64/CAT_ResampleSphericalSurf
 M CAT.maca64/CAT_ResampleSphericalSurfSPH
 M CAT.maca64/CAT_ResampleSurf
 M CAT.maca64/CAT_SelfIntersect
 M CAT.maca64/CAT_SeparatePolygon
 M CAT.maca64/CAT_SmoothConvexity
 M CAT.maca64/CAT_SulcusDepth
 M CAT.maca64/CAT_Surf2Sphere
 M CAT.maca64/CAT_Surf2Vol
 M CAT.maca64/CAT_SurfDistance
 M CAT.maca64/CAT_WarpSurf
 M CAT.maci64/CAT_3dVol2Surf
 M CAT.maci64/CAT_AddValuesToSurf
 M CAT.maci64/CAT_AverageSurfaces
 M CAT.maci64/CAT_BlurSurfHK
 M CAT.maci64/CAT_Central2Pial
 M CAT.maci64/CAT_DeformSurf
 M CAT.maci64/CAT_DumpCurv
 M CAT.maci64/CAT_DumpSurfArea
 M CAT.maci64/CAT_DumpSurfaceRatio
 M CAT.maci64/CAT_FixTopology
 M CAT.maci64/CAT_FractalDimension
 M CAT.maci64/CAT_Hausdorff
 M CAT.maci64/CAT_Isometize
 M CAT.maci64/CAT_MarchingCubesGenus0
 M CAT.maci64/CAT_MarkDefects
 M CAT.maci64/CAT_RefineMesh
 M CAT.maci64/CAT_ResampleSphericalSurf
 M CAT.maci64/CAT_ResampleSphericalSurfSPH
 M CAT.maci64/CAT_ResampleSurf
 M CAT.maci64/CAT_SelfIntersect
 M CAT.maci64/CAT_SeparatePolygon
 M CAT.maci64/CAT_SmoothConvexity
 M CAT.maci64/CAT_SulcusDepth
 M CAT.maci64/CAT_Surf2Sphere
 M CAT.maci64/CAT_Surf2Vol
 M CAT.maci64/CAT_SurfDistance
 M CAT.maci64/CAT_WarpSurf
 M CAT.w32/CAT_3dVol2Surf.exe
 M CAT.w32/CAT_AddValuesToSurf.exe
 M CAT.w32/CAT_AverageSurfaces.exe
 M CAT.w32/CAT_BlurSurfHK.exe
 M CAT.w32/CAT_Central2Pial.exe
 M CAT.w32/CAT_DeformSurf.exe
 M CAT.w32/CAT_DumpCurv.exe
 M CAT.w32/CAT_DumpSurfArea.exe
 M CAT.w32/CAT_DumpSurfaceRatio.exe
 M CAT.w32/CAT_FixTopology.exe
 M CAT.w32/CAT_FractalDimension.exe
 M CAT.w32/CAT_Hausdorff.exe
 M CAT.w32/CAT_Isometize.exe
 M CAT.w32/CAT_MarchingCubesGenus0.exe
 M CAT.w32/CAT_MarkDefects.exe
 M CAT.w32/CAT_RefineMesh.exe
 M CAT.w32/CAT_ResampleSphericalSurf.exe
 M CAT.w32/CAT_ResampleSphericalSurfSPH.exe
 M CAT.w32/CAT_ResampleSurf.exe
 M CAT.w32/CAT_SelfIntersect.exe
 M CAT.w32/CAT_SeparatePolygon.exe
 M CAT.w32/CAT_SmoothConvexity.exe
 M CAT.w32/CAT_SulcusDepth.exe
 M CAT.w32/CAT_Surf2Sphere.exe
 M CAT.w32/CAT_Surf2Vol.exe
 M CAT.w32/CAT_SurfDistance.exe
 M CAT.w32/CAT_WarpSurf.exe
 M CHANGES.txt
 M Contents.m
 M cat_conf_extopts.m
 M cat_main.m
 M cat_main1639.m
 M cat_stat_check_cov_old.m
 M cat_surf_createCS2.m
 M cat_surf_createCS3.m
 M cat_surf_fun.m
 M cat_surf_results.m
 M cat_surf_vol2surf.m
 M cat_vol_approx.m
 M cat_vol_smooth3X.m
 M doc/cat.html

(1) Changed: Set new recursice method as default in cat_vol_approx.m.
(2) Changed: Removed any "-linear" flags from calls to CAT_3dVol2Surf because
             this is not supported anymore.
(3) Changed: Set pbtsimple as default.
(4) Changed: Additionally keep largest structure and fill remaining holes
             incat_surf_createCS3.m before callung CAT_MarchingCubesGenus0.     
(5) Fixed:   Corrected handling of smoothing size if defined as vector in
             cat_vol_smooth3X.m.
(6) Fixed:   Corrected celltype in catstat_check_cov_old.m.
------------------------------------------------------------------------
r2509 | rdahnke | 2023-12-13 11:23:05

Changed paths:
 M CHANGES.txt

Changed:  Update new PBT simple pipeline with focus on the paired estimation of  
          multiple distance estimations to support partial volume effects also 
          with the simple voxel-based distance estimation cat_vbdist.
------------------------------------------------------------------------
r2499 | rdahnke | 2023-12-11 10:47:49

Changed paths:
 M CHANGES.txt

Changed:     Updated cat_vol_approx by revising the main function nn and adding
             also a new recursive approach. Added also a unit tested and extend
             the documentation. Although the new rec function performs best in 
             the unit test, real data test showed some strange side effects that
             need further investigation.     
------------------------------------------------------------------------
r2490 | rdahnke | 2023-12-11 10:46:35

Changed paths:
 M CHANGES.txt
 M cat_vol_approx.m

Changed:     Updated cat_vol_approx by revising the main function nn and adding
             also a new recursive approach. Added also a unit tested and extend
             the documentation. Although the new rec function performs best in 
             the unit test, real data test showed some strange side effects that
             need further investigation.     
------------------------------------------------------------------------
r2489 | gaser | 2023-12-05 09:13:23

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_vol_defs.m
 M doc/cat.html
 M doc/index.html

(1) Changed: Increased limit for maximum number of labels for categorical
             interpolation in cat_vol_def.m.
(2) Changed: Some corrections for authorships in references.
------------------------------------------------------------------------
r2485 | rdahnke | 2023-11-23 19:50:51

Changed paths:
 M CHANGES.txt
 M cat_main.m
 M cat_main1639.m
 M cat_main_cleanup.m
 M cat_run_job1639.m

Fixed:   Reset skull-stripping update in cat_main_cleanup (called from 
         cat_main[1639] to setting from r1981 and r2183 that includes update 
         of the brain mask but only in cases without skull-stripping. 
Fixed:   Tiny changes in cat_run_job1939.
------------------------------------------------------------------------
r2480 | dahnke | 2023-11-20 16:52:28

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m
 M cat_run_job1639.m
 M cat_stat_marks.m
 D cat_tst_qa201602.m
M  cat_vol_mimcalc.m
 M cat_vol_qa.m
 D cat_vol_qa2.m
 M cat_vol_qa201901.m

Large update of the quality control tools:  
Added new Version of image quality estimation cat_vol_qa that works now as hub 
to call different versions of the QC cat_vol_qa#(x) added here, with # as the 
year and month and an additional x that reference the updated versions corrected
for general problems observed in the new test framework. The test framework 
includes the (i) standard BWP, (ii) the BWP with simulated preprocessing error, 
(iii) IXI (aging), (iv) atlas (lesions), (iv) MR-ART (motion artifacts), and 
(v) a private library of real datasets of public/private projects/studies.  
Function was tested in cross-section, longitudinal, and batch.
            
1) Renamed:  Renamed cat_vol_qa to cat_vol_qa202205 (=deleted). 
             Renamed cat_vol_qa2 to cat_vol_qa (=replaced). 
             cat_vol_qa now only serves as hub to run specific qa versions
             cat_vol_qa# with # as data with year and month. 
2) Renamed:  Renamed cat_tst_qa201602 (=deleted) to cat_vol_qa20602 (=new) to 
             have all QC version together. 
3) Changed:  Added setting to choose QC version in QC batch and extended the 
             help in cat_conf_tools.   
4) Changed:  Updated cat_stat_marks settings and added temporary SIQR variants. 
5) New:      Added different processing version of cat_vol_qa#(x) available 
             via batch, where the x marks updated/debugged versions. 
6) New:      Added cat_vol_normer to normalize quality ratings within protocols 
             for outlier detection. 

------------------------------------------------------------------------
r2479 | gaser | 2023-11-14 19:40:19

Changed paths:
 M CHANGES.txt
 M cat_io_data2mat.m
 M cat_run.m
 M cat_vol_img2mip.m
 M cat_vol_laterality_index.m

Changed: Suppress progress bar for smaller sample in  cat_vol_data2mat.m.
Changed: Added correction of origin for laterality images in cat_vol_img2mip.m.
Changed: Updated cat_vol_laterality_index.m.
------------------------------------------------------------------------
r2478 | gaser | 2023-11-13 15:41:36

Changed paths:
 M CHANGES.txt
 M cat_run_job1639.m
 M cat_vol_laterality_index.m
A  templates_MNI152NLin2009cAsym/y_MNI152NLin2009cAsym_to_MNI152NLin2009cSym.nii

Added:   Added new deformation field for getting symmetrical spatially registered 
         images for estimating laterality index.
Changed: Updated path of symmetrical deformation field.
------------------------------------------------------------------------
r2477 | gaser | 2023-11-13 11:35:53

Changed paths:
 M CHANGES.txt
 M cat_vol_defs.m
 M cat_vol_laterality_index.m

Changed: Updated function cat_vol_laterality_index. to calculate laterality
         index for VBM data.
------------------------------------------------------------------------
r2476 | gaser | 2023-11-10 16:02:32

Changed paths:
MM CHANGES.txt
MM cat_batch_bids.sh
MM cat_batch_cat.sh
MM cat_batch_long.sh
 M cat_progress_bar.m
A  cat_vol_laterality_index.m

Changed: Added some flags to waitbar window in cat_progressbar to prevent 
         unwished popping up of the window.
Added:   New function to calculate laterality index for VBM data.
------------------------------------------------------------------------
r2475 | gaser | 2023-11-10 12:08:18

Changed paths:
 M CHANGES.txt
 M cat_batch_bids.sh
 M cat_batch_cat.sh
 M cat_batch_long.sh

Changed: Small corrections for shell scripts cat_batch*.sh
------------------------------------------------------------------------
r2473 | gaser | 2023-11-10 09:41:11

Changed paths:
 M CHANGES.txt
 M check_pipeline.sh
 M check_pipeline_homogeneity.m

Changed: Updated check_pipeline.sh and added checks for xml-files.
Changed: Added check whether reöease string is empty in check_pipeline_homogeneity.m
------------------------------------------------------------------------
r2472 | rdahnke | 2023-11-09 10:53:16

Changed paths:
 M CHANGES.txt
 M cat_io_rerun.m
 M cat_vol_pbtsimple.m
 M cat_vol_resize.m

1) Changed:  Added new thickness-based correction in cat_vol_pbtsimple to better
             interpretative WM boundary within the GM/WM partial volume range.
2) Fixed:    Corrected bug in cat_vol_resize. 
3) Changed:  Optimised command-line output of cat_io_rerun. 
------------------------------------------------------------------------
r2471 | gaser | 2023-11-08 21:46:48

Changed paths:
 M CHANGES.txt

Changed: Set default surface processing back to 22 (CS2).
Added:   New function to calculate laterality index for volumes.
Fixed:   Corrected error in cat_batch_bids.sh where cat12 folder was not correctly
         defined.
------------------------------------------------------------------------
r2470 | gaser | 2023-11-08 21:43:04

Changed paths:
 M CHANGES.txt
 M cat_batch_bids.sh
 M cat_defaults.m
 M cat_surf_laterality_index.m
 M templates_MNI152NLin2009cAsym/thalamic_nuclei.txt

Changed: Set default surface processing back to 22 (CS2).
Added:   New function to calculate laterality index for volumes.
Fixed:   Corrected error in cat_batch_bids.sh wehre cat12 folder was not correctly
         defined.
------------------------------------------------------------------------
r2467 | rdahnke | 2023-10-04 22:50:35

Changed paths:
 M CAT.maci64/CAT_MarchingCubesGenus0
 M CHANGES.txt
 M cat_vol_eidist.c
 M cat_vol_eidist.mexmaci64
 M cat_vol_pbt.m
 M cat_vol_pbtsimple.m

1) Changed:    Restructured cat_vol_pbtsimple function with additional smoothing
               and additional interpolation to support partial volume effects 
               also for the simple grid-based distance estimation.  
2) Changed:    Small corrections in special (unused) cases in cat_vol_pbt.
3) Fixed:      Corrections in cat_vol_eidist.c to handle partial volume effects
               in the initial preparation! 
4) Changed:    Uploaded CAT.maci64/CAT_MarchingCubesGenus0 function.                
------------------------------------------------------------------------
r2465 | rdahnke | 2023-09-30 13:29:22

Changed paths:
 M CHANGES.txt
 M cat_conf_extopts.m
 M cat_main.m
 M cat_run_job1639.m
 M cat_surf_createCS3.m
 M cat_surf_renderv.m
 M cat_system.m
 M cat_vol_mimcalc.m

1) New:     Added cat_vol_pbtsimple in cat_surf_createCS3 as simplified of the 
            regular PBT function that can be accessed in the developer GUI 
            (cat_conf_extopts). Updated call of CAT_MarchingCubesGenus0.
2) Fixed:   Added missing parameter in cat_main.
3) Changed: Added suggestion to error message in cat_run_job1639.
4) Fixed:   Corrected bug in cat_surf_renderv and cat_vol_mimcalc.
5) Fixed:   Corrected bugs in cat_system in MAC 
------------------------------------------------------------------------
r2464 | gaser | 2023-09-28 21:56:29

Changed paths:
 M CHANGES.txt
 M cat12.sh
 M cat_batch_cat.sh
 M cat_vbdist.c
 M cat_vol_eidist.c
 M cat_vol_laplace3.c
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M check_pipeline.sh
 M distribute_to_server.sh

Changed: Removed old SVN version information.
------------------------------------------------------------------------
r2463 | gaser | 2023-09-13 02:25:48

Changed paths:
 M .gitattributes
 M CHANGES.txt
 M cat_io_data2mat.m
 M cat_system.m

Changed: Compiled CAT binaries.
Changed: Also consider unmodulated ^wp-images for ROI analysis.
Changed: Slight modifications to cat_vol_slice_overlay_ui.m and 
         cat_surf_results.m
Fixed:   Added missing default for number of processors to cat_batch_cat.sh.
------------------------------------------------------------------------
r2462 | gaser | 2023-09-07 11:58:41

Changed paths:
 M .gitattributes
 M CHANGES.txt

Changed: Compiled CAT binaries.
Changed: Also consider unmodulated ^wp-images for ROI analysis.
Changed: Slight modifications to cat_vol_slice_overlay_ui.m and 
         cat_surf_results.m
Fixed:   Added missing default for number of processors to cat_batch_cat.sh.
------------------------------------------------------------------------
r2461 | gaser | 2023-09-07 11:56:37

Changed paths:
 M CHANGES.txt

Changed: Compiled CAT binaries.
Changed: Also consider unmodulated ^wp-images for ROI analysis.
Changed: Slight modifications to cat_vol_slice_overlay_ui.m and 
         cat_surf_results.m
Fixed:   Added missing default for number of processors to cat_batch_cat.sh.
------------------------------------------------------------------------
r2460 | gaser | 2023-09-07 11:54:38

Changed paths:
 M CAT.glnx86/CAT_3dVol2Surf
 M CAT.glnx86/CAT_AddValuesToSurf
 M CAT.glnx86/CAT_AverageSurfaces
 M CAT.glnx86/CAT_BlurSurfHK
 M CAT.glnx86/CAT_Central2Pial
 M CAT.glnx86/CAT_DeformSurf
 M CAT.glnx86/CAT_DumpCurv
 M CAT.glnx86/CAT_DumpSurfArea
 M CAT.glnx86/CAT_DumpSurfaceRatio
 M CAT.glnx86/CAT_FixTopology
 M CAT.glnx86/CAT_FractalDimension
 M CAT.glnx86/CAT_Hausdorff
 M CAT.glnx86/CAT_Isometize
 M CAT.glnx86/CAT_MarchingCubesGenus0
 M CAT.glnx86/CAT_MarkDefects
 M CAT.glnx86/CAT_RefineMesh
 M CAT.glnx86/CAT_ResampleSphericalSurf
 M CAT.glnx86/CAT_ResampleSphericalSurfSPH
 M CAT.glnx86/CAT_ResampleSurf
 M CAT.glnx86/CAT_SelfIntersect
 M CAT.glnx86/CAT_SeparatePolygon
 M CAT.glnx86/CAT_SmoothConvexity
 M CAT.glnx86/CAT_SulcusDepth
 M CAT.glnx86/CAT_Surf2Sphere
 M CAT.glnx86/CAT_Surf2Vol
 M CAT.glnx86/CAT_SurfDistance
 M CAT.glnx86/CAT_WarpSurf
 M CAT.maca64/CAT_3dVol2Surf
 M CAT.maca64/CAT_AddValuesToSurf
 M CAT.maca64/CAT_AverageSurfaces
 M CAT.maca64/CAT_BlurSurfHK
 M CAT.maca64/CAT_Central2Pial
 M CAT.maca64/CAT_DeformSurf
 M CAT.maca64/CAT_DumpCurv
 M CAT.maca64/CAT_DumpSurfArea
 M CAT.maca64/CAT_DumpSurfaceRatio
 M CAT.maca64/CAT_FixTopology
 M CAT.maca64/CAT_FractalDimension
 M CAT.maca64/CAT_Hausdorff
 M CAT.maca64/CAT_Isometize
 M CAT.maca64/CAT_MarchingCubesGenus0
 M CAT.maca64/CAT_MarkDefects
 M CAT.maca64/CAT_RefineMesh
 M CAT.maca64/CAT_ResampleSphericalSurf
 M CAT.maca64/CAT_ResampleSphericalSurfSPH
 M CAT.maca64/CAT_ResampleSurf
 M CAT.maca64/CAT_SelfIntersect
 M CAT.maca64/CAT_SeparatePolygon
 M CAT.maca64/CAT_SmoothConvexity
 M CAT.maca64/CAT_SulcusDepth
 M CAT.maca64/CAT_Surf2Sphere
 M CAT.maca64/CAT_Surf2Vol
 M CAT.maca64/CAT_SurfDistance
 M CAT.maca64/CAT_WarpSurf
 M CAT.maci64/CAT_3dVol2Surf
 M CAT.maci64/CAT_AddValuesToSurf
 M CAT.maci64/CAT_AverageSurfaces
 M CAT.maci64/CAT_BlurSurfHK
 M CAT.maci64/CAT_Central2Pial
 M CAT.maci64/CAT_DeformSurf
 M CAT.maci64/CAT_DumpCurv
 M CAT.maci64/CAT_DumpSurfArea
 M CAT.maci64/CAT_DumpSurfaceRatio
 M CAT.maci64/CAT_FixTopology
 M CAT.maci64/CAT_FractalDimension
 M CAT.maci64/CAT_Hausdorff
 M CAT.maci64/CAT_Isometize
 M CAT.maci64/CAT_MarchingCubesGenus0
 M CAT.maci64/CAT_MarkDefects
 M CAT.maci64/CAT_RefineMesh
 M CAT.maci64/CAT_ResampleSphericalSurf
 M CAT.maci64/CAT_ResampleSphericalSurfSPH
 M CAT.maci64/CAT_ResampleSurf
 M CAT.maci64/CAT_SelfIntersect
 M CAT.maci64/CAT_SeparatePolygon
 M CAT.maci64/CAT_SmoothConvexity
 M CAT.maci64/CAT_SulcusDepth
 M CAT.maci64/CAT_Surf2Sphere
 M CAT.maci64/CAT_Surf2Vol
 M CAT.maci64/CAT_SurfDistance
 M CAT.maci64/CAT_WarpSurf
 M CAT.w32/CAT_3dVol2Surf.exe
 M CAT.w32/CAT_AddValuesToSurf.exe
 M CAT.w32/CAT_AverageSurfaces.exe
 M CAT.w32/CAT_BlurSurfHK.exe
 M CAT.w32/CAT_Central2Pial.exe
 M CAT.w32/CAT_DeformSurf.exe
 M CAT.w32/CAT_DumpCurv.exe
 M CAT.w32/CAT_DumpSurfArea.exe
 M CAT.w32/CAT_DumpSurfaceRatio.exe
 M CAT.w32/CAT_FixTopology.exe
 M CAT.w32/CAT_FractalDimension.exe
 M CAT.w32/CAT_Hausdorff.exe
 M CAT.w32/CAT_Isometize.exe
 M CAT.w32/CAT_MarchingCubesGenus0.exe
 M CAT.w32/CAT_MarkDefects.exe
 M CAT.w32/CAT_RefineMesh.exe
 M CAT.w32/CAT_ResampleSphericalSurf.exe
 M CAT.w32/CAT_ResampleSphericalSurfSPH.exe
 M CAT.w32/CAT_ResampleSurf.exe
 M CAT.w32/CAT_SelfIntersect.exe
 M CAT.w32/CAT_SeparatePolygon.exe
 M CAT.w32/CAT_SmoothConvexity.exe
 M CAT.w32/CAT_SulcusDepth.exe
 M CAT.w32/CAT_Surf2Sphere.exe
 M CAT.w32/CAT_Surf2Vol.exe
 M CAT.w32/CAT_SurfDistance.exe
 M CAT.w32/CAT_WarpSurf.exe
 M CHANGES.txt
 M cat_batch_cat.sh
 M cat_main_amap1639.m
 M cat_stat_analyze_ROIs.m
 M cat_surf_results.m
 M cat_vol_slice_overlay.m

Changed: Compiled CAT binaries.
Changed: Also consider unmodulated ^wp-images for ROI analysis.
Changed: Slight modifications to cat_vol_slice_overlay_ui.m and 
         cat_surf_results.m
Fixed:   Added missing default for number of processors to cat_batch_cat.sh.
------------------------------------------------------------------------
r2459 | gaser | 2023-09-01 18:09:47

Changed paths:
 M CHANGES.txt
 M cat_io_xml.m
 M cat_main_registration.m
 M cat_vol_img2mip.m

Changed: Added some range correction to cat_vol_img2mip.m.
Fixed:   Skipped some matlab-checking in cat_io_xml.m that was not working for 
         newer Matlab versions.
Fixed:   Changed data type in cat_main_registration, because type was not always
         set correctly.
------------------------------------------------------------------------
r2458 | gaser | 2023-08-22 17:31:07

Changed paths:
 M CHANGES.txt
 M Makefile
R  html/images/CAT_Poster.jpg -> doc/images/CAT_Poster.jpg
 M spm_cat12.m

Fixed: Moved CAT_Poster.png to doc/images and changed path in spm_cat12.m.
------------------------------------------------------------------------
r2457 | gaser | 2023-08-22 09:18:09

Changed paths:
 M CHANGES.txt
 M cat_batch_cat.m
 M cat_batch_cat.sh

Fixed: Use quoted filenames in temporary files to consider whitespaces in names
       in cat_batch_cat.*.
------------------------------------------------------------------------
r2456 | gaser | 2023-08-21 09:28:54

Changed paths:
 M CHANGES.txt
 M cat_batch_cat.sh

Fixed: Corrected handling of processors and files with whitespaces in names in 
       cat_batch_cat.sh.
------------------------------------------------------------------------
r2455 | gaser | 2023-08-18 18:37:17

Changed paths:
 M CHANGES.txt
 M cat_main1639.m
 M cat_plot_scatter.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c

Changed: Updated help text.
Changed: Added rng-init for jittered scatter plot to cat_plot_scatter.m.
------------------------------------------------------------------------
r2454 | rdahnke | 2023-08-09 12:14:31

Changed paths:
 M .gitignore
 M CHANGES.txt
 M cat_surf_render2.m
 M spm_cat12.m

1) Fixed:    Corrected poster background bugs in Octave. 
------------------------------------------------------------------------
r2452 | gaser | 2023-08-08 11:05:49

Changed paths:
 M CHANGES.txt
A  mexmaca/@file_array/private/file2mat.mex
A  mexmaca/@file_array/private/init.mex
A  mexmaca/@file_array/private/mat2file.mex
A  mexmaca/@gifti/private/zstream.mex
A  mexmaca/@xmltree/private/xml_findstr.mex
A  mexmaca/spm_add.mex
A  mexmaca/spm_brainwarp.mex
A  mexmaca/spm_bsplinc.mex
A  mexmaca/spm_bsplins.mex
A  mexmaca/spm_bwlabel.mex
A  mexmaca/spm_cat.mex
A  mexmaca/spm_conv_vol.mex
A  mexmaca/spm_diffeo.mex
A  mexmaca/spm_dilate_erode.mex
A  mexmaca/spm_existfile.mex
A  mexmaca/spm_field.mex
A  mexmaca/spm_gamrnd.mex
A  mexmaca/spm_get_lm.mex
A  mexmaca/spm_global.mex
A  mexmaca/spm_gmmlib.mex
A  mexmaca/spm_hist.mex
A  mexmaca/spm_hist2.mex
A  mexmaca/spm_jsonread.mex
A  mexmaca/spm_krutil.mex
A  mexmaca/spm_mesh_geodesic.mex
A  mexmaca/spm_mesh_reduce.mex
A  mexmaca/spm_mesh_utils.mex
A  mexmaca/spm_mrf.mex
A  mexmaca/spm_project.mex
A  mexmaca/spm_render_vol.mex
A  mexmaca/spm_resels_vol.mex
A  mexmaca/spm_sample_vol.mex
A  mexmaca/spm_slice_vol.mex
A  mexmaca/spm_unlink.mex
A  mexmaca/spm_voronoi.mex

Added: Added some missing mex-files for Octave for Apple Silicon.
------------------------------------------------------------------------
r2449 | gaser | 2023-08-08 10:58:44

Changed paths:
 M CHANGES.txt
 M Makefile
 M cat_conf_factorial.m
 M cat_io_report.m
 M cat_main_reportfig.m
 M cat_run.m
 M cat_spm_results_ui.m
 M cat_stat_spm.m
 M cat_surf_createCS3.m
 M cat_surf_renderv.m
 D mexmaci/@file_array/Contents.m
 D mexmaci/@file_array/cat.m
 D mexmaci/@file_array/ctranspose.m
 D mexmaci/@file_array/disp.m
 D mexmaci/@file_array/display.m
 D mexmaci/@file_array/double.m
 D mexmaci/@file_array/end.m
 D mexmaci/@file_array/fieldnames.m
 D mexmaci/@file_array/file_array.m
 D mexmaci/@file_array/full.m
 D mexmaci/@file_array/horzcat.m
 D mexmaci/@file_array/initialise.m
 D mexmaci/@file_array/isnan.m
 D mexmaci/@file_array/length.m
 D mexmaci/@file_array/loadobj.m
 D mexmaci/@file_array/ndims.m
 D mexmaci/@file_array/numel.m
 D mexmaci/@file_array/numeric.m
 D mexmaci/@file_array/permute.m
 D mexmaci/@file_array/private/Makefile
 D mexmaci/@file_array/private/datatypes.m
 D mexmaci/@file_array/private/dim.m
 D mexmaci/@file_array/private/dtype.m
 D mexmaci/@file_array/private/file2mat.c
 D mexmaci/@file_array/private/file2mat.m
 D mexmaci/@file_array/private/file2mat.mexa64
 D mexmaci/@file_array/private/file2mat.mexmaci64
 D mexmaci/@file_array/private/file2mat.mexw32
 D mexmaci/@file_array/private/file2mat.mexw64
 D mexmaci/@file_array/private/fname.m
 D mexmaci/@file_array/private/init.c
 D mexmaci/@file_array/private/init.m
 D mexmaci/@file_array/private/init.mexa64
 D mexmaci/@file_array/private/init.mexmaci64
 D mexmaci/@file_array/private/init.mexw32
 D mexmaci/@file_array/private/init.mexw64
 D mexmaci/@file_array/private/mat2file.c
 D mexmaci/@file_array/private/mat2file.m
 D mexmaci/@file_array/private/mat2file.mexa64
 D mexmaci/@file_array/private/mat2file.mexmaci64
 D mexmaci/@file_array/private/mat2file.mexw32
 D mexmaci/@file_array/private/mat2file.mexw64
 D mexmaci/@file_array/private/mystruct.m
 D mexmaci/@file_array/private/offset.m
 D mexmaci/@file_array/private/permission.m
 D mexmaci/@file_array/private/resize_scales.m
 D mexmaci/@file_array/private/scl_inter.m
 D mexmaci/@file_array/private/scl_slope.m
 D mexmaci/@file_array/reshape.m
 D mexmaci/@file_array/size.m
 D mexmaci/@file_array/subsasgn.m
 D mexmaci/@file_array/subsref.m
 D mexmaci/@file_array/transpose.m
 D mexmaci/@file_array/vertcat.m
 D mexmaci/@gifti/Contents.m
 D mexmaci/@gifti/display.m
 D mexmaci/@gifti/export.m
 D mexmaci/@gifti/fieldnames.m
 D mexmaci/@gifti/gifti.m
 D mexmaci/@gifti/isfield.m
 D mexmaci/@gifti/plot.m
 D mexmaci/@gifti/private/Makefile
 D mexmaci/@gifti/private/base64decode.m
 D mexmaci/@gifti/private/base64encode.m
 D mexmaci/@gifti/private/dunzip.m
 D mexmaci/@gifti/private/dzip.m
 D mexmaci/@gifti/private/getdict.m
 D mexmaci/@gifti/private/isintent.m
 D mexmaci/@gifti/private/miniz.c
 D mexmaci/@gifti/private/mvtk_read.m
 D mexmaci/@gifti/private/mvtk_write.m
 D mexmaci/@gifti/private/mz3_read.m
 D mexmaci/@gifti/private/mz3_write.m
 D mexmaci/@gifti/private/obj_read.m
 D mexmaci/@gifti/private/off_read.m
 D mexmaci/@gifti/private/ply_read.m
 D mexmaci/@gifti/private/read_freesurfer_file.m
 D mexmaci/@gifti/private/read_gifti_file.m
 D mexmaci/@gifti/private/stl_read.m
 D mexmaci/@gifti/private/zstream.c
 D mexmaci/@gifti/private/zstream.m
 D mexmaci/@gifti/private/zstream.mexa64
 D mexmaci/@gifti/private/zstream.mexmaci64
 D mexmaci/@gifti/private/zstream.mexw32
 D mexmaci/@gifti/private/zstream.mexw64
 D mexmaci/@gifti/save.m
 D mexmaci/@gifti/saveas.m
 D mexmaci/@gifti/struct.m
 D mexmaci/@gifti/subsasgn.m
 D mexmaci/@gifti/subsref.m
 M spm_cat12.m

Added:   Added some missing mex-files for Octave for Apple Silicon.
Deleted: Removed unnecessary files from mex* folders.
Changed: Changed fileformat for saving SPM.mat depending on file size.
Changed: Updated print of report file for Octave.
Changed: Added waiting time to loadSurf subfunction in cat_surf_createCS3.m
         to consider potential delay in file writing.
Fixed:   Corrected typo in spm_cat12.m.

------------------------------------------------------------------------
r2448 | rdahnke | 2023-08-07 16:47:25

Changed paths:
 M CHANGES.txt
 M spm_cat12.m

1)  Changed:   Added poster background.

------------------------------------------------------------------------
r2447 | rdahnke | 2023-08-07 16:22:47

########################################################################
Please note that this commit was removed!
########################################################################
Changed paths:
 M CHANGES.txt
 M cat_main1639.m
 M cat_main_registration.m
 M cat_main_write.m
 M cat_run.m
 M cat_run_job1639.m

1)  Changed:   Enhanced skull-stripping background detection to support non-
               zero background intensities. Test for high intensity backgrounds
               only in case of no skull-stripping. Update skull-stripping expert 
               message (line 285-525).
2)  Changed:   Replaced slice-wise spm_smoothto8bit function and small filter 
               size modification (line 537-628). 
3)  Changed:   Improved skull-stripped affine input case (line 594-601).               
4)  Changed:   Modified input of COM estimation by using the initial skull-
               stripping (WM-like tissue) that is error-prone but still better 
               than using the full head (line 674-689).
5)  Changed:   Save affine parameters (line 694-. 
6)  Changed:   Use fine affine registration (maff8) not in case of skull-
               stripped data (line 904-908).
7)  Changed:   Try to use simplified brain model without tissue separation for 
               maff8 to avoid side effects by tissue atrophy (line 918-933).
8)  Changed:   Try to use skull-stripping mask maffreg                
9)  Fixed:     Corrected bug in lazy processing setup in cat_run.  
10) Fixed:     Corrected bug in writing atlas results into the right space in 
               cat_main_write and cat_main_registration. 
11) Changed:   Added final affine registration based on the final brain mask in 
               cat_main_registration and cat_main.
------------------------------------------------------------------------
r2446 | gaser | 2023-08-07 11:23:26

Changed paths:
 M CHANGES.txt
A  mexmaca/cat_amap.mex
A  mexmaca/cat_ornlm.mex
A  mexmaca/cat_sanlm.mex
A  mexmaca/cat_vbdist.mex
A  mexmaca/cat_vol_downcut.mex
A  mexmaca/cat_vol_eidist.mex
A  mexmaca/cat_vol_genus0.mex
A  mexmaca/cat_vol_gradient3.mex
A  mexmaca/cat_vol_interp3f.mex
A  mexmaca/cat_vol_laplace3.mex
A  mexmaca/cat_vol_laplace3R.mex
A  mexmaca/cat_vol_localstat.mex
A  mexmaca/cat_vol_median3.mex
A  mexmaca/cat_vol_median3c.mex
A  mexmaca/cat_vol_pbtp.mex
A  mexmaca/cat_vol_pbtp2.mex
A  mexmaca/cat_vol_simgrow.mex

Added:   Created new mex-folder for octave for Apple Silicon.
------------------------------------------------------------------------
r2445 | gaser | 2023-08-07 11:22:24

Changed paths:
 M CHANGES.txt
 M cat_io_xml.m
 M cat_long_report.m
 M cat_run.m
 M cat_run_job1639.m
 M cat_stat_histth.m
 M cat_vol_imcalc.m
A  mexmaci/@file_array/Contents.m
A  mexmaci/@file_array/cat.m
A  mexmaci/@file_array/ctranspose.m
A  mexmaci/@file_array/disp.m
A  mexmaci/@file_array/display.m
A  mexmaci/@file_array/double.m
A  mexmaci/@file_array/end.m
A  mexmaci/@file_array/fieldnames.m
A  mexmaci/@file_array/file_array.m
A  mexmaci/@file_array/full.m
A  mexmaci/@file_array/horzcat.m
A  mexmaci/@file_array/initialise.m
A  mexmaci/@file_array/isnan.m
A  mexmaci/@file_array/length.m
A  mexmaci/@file_array/loadobj.m
A  mexmaci/@file_array/ndims.m
A  mexmaci/@file_array/numel.m
A  mexmaci/@file_array/numeric.m
A  mexmaci/@file_array/permute.m
A  mexmaci/@file_array/private/Makefile
A  mexmaci/@file_array/private/datatypes.m
A  mexmaci/@file_array/private/dim.m
A  mexmaci/@file_array/private/dtype.m
A  mexmaci/@file_array/private/file2mat.c
A  mexmaci/@file_array/private/file2mat.m
A  mexmaci/@file_array/private/file2mat.mex
A  mexmaci/@file_array/private/file2mat.mexa64
A  mexmaci/@file_array/private/file2mat.mexmaci64
A  mexmaci/@file_array/private/file2mat.mexw32
A  mexmaci/@file_array/private/file2mat.mexw64
A  mexmaci/@file_array/private/fname.m
A  mexmaci/@file_array/private/init.c
A  mexmaci/@file_array/private/init.m
A  mexmaci/@file_array/private/init.mex
A  mexmaci/@file_array/private/init.mexa64
A  mexmaci/@file_array/private/init.mexmaci64
A  mexmaci/@file_array/private/init.mexw32
A  mexmaci/@file_array/private/init.mexw64
A  mexmaci/@file_array/private/mat2file.c
A  mexmaci/@file_array/private/mat2file.m
A  mexmaci/@file_array/private/mat2file.mex
A  mexmaci/@file_array/private/mat2file.mexa64
A  mexmaci/@file_array/private/mat2file.mexmaci64
A  mexmaci/@file_array/private/mat2file.mexw32
A  mexmaci/@file_array/private/mat2file.mexw64
A  mexmaci/@file_array/private/mystruct.m
A  mexmaci/@file_array/private/offset.m
A  mexmaci/@file_array/private/permission.m
A  mexmaci/@file_array/private/resize_scales.m
A  mexmaci/@file_array/private/scl_inter.m
A  mexmaci/@file_array/private/scl_slope.m
A  mexmaci/@file_array/reshape.m
A  mexmaci/@file_array/size.m
A  mexmaci/@file_array/subsasgn.m
A  mexmaci/@file_array/subsref.m
A  mexmaci/@file_array/transpose.m
A  mexmaci/@file_array/vertcat.m
A  mexmaci/@gifti/Contents.m
A  mexmaci/@gifti/display.m
A  mexmaci/@gifti/export.m
A  mexmaci/@gifti/fieldnames.m
A  mexmaci/@gifti/gifti.m
A  mexmaci/@gifti/isfield.m
A  mexmaci/@gifti/plot.m
A  mexmaci/@gifti/private/Makefile
A  mexmaci/@gifti/private/base64decode.m
A  mexmaci/@gifti/private/base64encode.m
A  mexmaci/@gifti/private/dunzip.m
A  mexmaci/@gifti/private/dzip.m
A  mexmaci/@gifti/private/getdict.m
A  mexmaci/@gifti/private/isintent.m
A  mexmaci/@gifti/private/miniz.c
A  mexmaci/@gifti/private/mvtk_read.m
A  mexmaci/@gifti/private/mvtk_write.m
A  mexmaci/@gifti/private/mz3_read.m
A  mexmaci/@gifti/private/mz3_write.m
A  mexmaci/@gifti/private/obj_read.m
A  mexmaci/@gifti/private/off_read.m
A  mexmaci/@gifti/private/ply_read.m
A  mexmaci/@gifti/private/read_freesurfer_file.m
A  mexmaci/@gifti/private/read_gifti_file.m
A  mexmaci/@gifti/private/stl_read.m
A  mexmaci/@gifti/private/zstream.c
A  mexmaci/@gifti/private/zstream.m
A  mexmaci/@gifti/private/zstream.mex
A  mexmaci/@gifti/private/zstream.mexa64
A  mexmaci/@gifti/private/zstream.mexmaci64
A  mexmaci/@gifti/private/zstream.mexw32
A  mexmaci/@gifti/private/zstream.mexw64
A  mexmaci/@gifti/save.m
A  mexmaci/@gifti/saveas.m
A  mexmaci/@gifti/struct.m
A  mexmaci/@gifti/subsasgn.m
A  mexmaci/@gifti/subsref.m
A  mexmaci/cat_amap.mex
A  mexmaci/cat_ornlm.mex
A  mexmaci/cat_sanlm.mex
A  mexmaci/cat_vbdist.mex
A  mexmaci/cat_vol_downcut.mex
A  mexmaci/cat_vol_eidist.mex
A  mexmaci/cat_vol_genus0.mex
A  mexmaci/cat_vol_gradient3.mex
A  mexmaci/cat_vol_interp3f.mex
A  mexmaci/cat_vol_laplace3.mex
A  mexmaci/cat_vol_laplace3R.mex
A  mexmaci/cat_vol_localstat.mex
A  mexmaci/cat_vol_median3.mex
A  mexmaci/cat_vol_median3c.mex
A  mexmaci/cat_vol_pbtp.mex
A  mexmaci/cat_vol_pbtp2.mex
A  mexmaci/cat_vol_simgrow.mex
A  mexmaci/spm_add.mex
A  mexmaci/spm_bsplinc.mex
A  mexmaci/spm_bsplins.mex
A  mexmaci/spm_bwlabel.mex
A  mexmaci/spm_cat.mex
A  mexmaci/spm_conv_vol.mex
A  mexmaci/spm_diffeo.mex
A  mexmaci/spm_dilate_erode.mex
A  mexmaci/spm_existfile.mex
A  mexmaci/spm_field.mex
A  mexmaci/spm_gamrnd.mex
A  mexmaci/spm_get_lm.mex
A  mexmaci/spm_global.mex
A  mexmaci/spm_hist.mex
A  mexmaci/spm_hist2.mex
A  mexmaci/spm_jsonread.mex
A  mexmaci/spm_krutil.mex
A  mexmaci/spm_mesh_reduce.mex
A  mexmaci/spm_mesh_utils.mex
A  mexmaci/spm_mrf.mex
A  mexmaci/spm_project.mex
A  mexmaci/spm_render_vol.mex
A  mexmaci/spm_resels_vol.mex
A  mexmaci/spm_sample_vol.mex
A  mexmaci/spm_slice_vol.mex
A  mexmaci/spm_unlink.mex
A  mexmaci/spm_voronoi.mex
 M spm_cat12.m

Added:   Created new mex-folders for octave for different systems.
Fixed:   Corrected small indexing error in cat_stat_histh.m.
Changed: Replaced strlength by lenght in cat_run_job1639.m because it's not 
         defined for older Matlab versions.
Changed: Added check for data_xml field in cat_long_report.m.
Changed: Removed java dependency in cat_io_xml.m.
------------------------------------------------------------------------
r2443 | gaser | 2023-07-17 15:39:01

Changed paths:
D  ..bfg-report/2023-07-17/13-58-11/cache-stats.txt
D  ..bfg-report/2023-07-17/13-58-11/deleted-files.txt
D  ..bfg-report/2023-07-17/13-58-11/object-id-map.old-new.txt
D  ..bfg-report/2023-07-17/13-58-11/protected-dirt/c15198e6-HEAD.csv
 M .gitattributes
 M CHANGES.txt
D  templates_external/MNI152NLin2009cAsym.nii
D  templates_external/MNI152NLin2009cSym.nii
D  templates_external/MNI152NLin6Asym.nii
D  templates_external/MNIColin27.nii
D  templates_external/y_IXI555Dartel_to_MNI152NLin2009cAsym.nii
D  templates_external/y_MNI152NLin2009cSym_to_MNI152NLin2009cAsym.nii
D  templates_external/y_MNI152NLin6Asym_to_MNI152NLin2009cAsym.nii
D  templates_external/y_MNIColin27_to_MNI152NLin2009cAsym.nii
D  templates_external/y_fMNI152NLin2009cAsym_to_MNI152NLin2009cAsym.nii
D  templates_volumes_not_distributed/aal.csv
D  templates_volumes_not_distributed/aal.nii
D  templates_volumes_not_distributed/aal.txt
D  templates_volumes_not_distributed/anatomy.csv
D  templates_volumes_not_distributed/anatomy.nii
D  templates_volumes_not_distributed/anatomy.txt
D  templates_volumes_not_distributed/aparc_DKT40.nii
D  templates_volumes_not_distributed/aparc_a2009s.nii
D  templates_volumes_old/Schaefer2018_100Parcels_17Networks_order.csv
D  templates_volumes_old/Schaefer2018_100Parcels_17Networks_order.nii
D  templates_volumes_old/Schaefer2018_200Parcels_17Networks_order.csv
D  templates_volumes_old/Schaefer2018_200Parcels_17Networks_order.nii
D  templates_volumes_old/Schaefer2018_400Parcels_17Networks_order.csv
D  templates_volumes_old/Schaefer2018_400Parcels_17Networks_order.nii
D  templates_volumes_old/Schaefer2018_600Parcels_17Networks_order.csv
D  templates_volumes_old/Schaefer2018_600Parcels_17Networks_order.nii
D  templates_volumes_old/TPM_Age11.5.nii
D  templates_volumes_old/Template_0_IXI555_MNI152_GS.nii
D  templates_volumes_old/Template_1_IXI555_MNI152.nii
D  templates_volumes_old/Template_1_IXI555_MNI152_GS.nii
D  templates_volumes_old/Template_2_IXI555_MNI152.nii
D  templates_volumes_old/Template_2_IXI555_MNI152_GS.nii
D  templates_volumes_old/Template_3_IXI555_MNI152.nii
D  templates_volumes_old/Template_3_IXI555_MNI152_GS.nii
D  templates_volumes_old/Template_4_IXI555_MNI152.nii
D  templates_volumes_old/Template_4_IXI555_MNI152_GS.nii
D  templates_volumes_old/Template_5_IXI555_MNI152.nii
D  templates_volumes_old/Template_6_IXI555_MNI152.nii
D  templates_volumes_old/Template_T1_IXI555_MNI152_GS.nii
D  templates_volumes_old/aal3.csv
D  templates_volumes_old/aal3.nii
D  templates_volumes_old/aal3.txt
D  templates_volumes_old/anatomy3.csv
D  templates_volumes_old/anatomy3.nii
D  templates_volumes_old/anatomy3.txt
D  templates_volumes_old/brainmask.nii
D  templates_volumes_old/cat.nii
D  templates_volumes_old/cat_strokelesions_ATLAS303.nii
D  templates_volumes_old/cat_wmh.nii
D  templates_volumes_old/cat_wmh_miccai2017.nii
D  templates_volumes_old/cobra.csv
D  templates_volumes_old/cobra.nii
D  templates_volumes_old/cobra.txt
D  templates_volumes_old/hammers.csv
D  templates_volumes_old/hammers.nii
D  templates_volumes_old/hammers.txt
D  templates_volumes_old/ibsr.csv
D  templates_volumes_old/ibsr.nii
D  templates_volumes_old/ibsr.txt
D  templates_volumes_old/julichbrain.csv
D  templates_volumes_old/julichbrain.nii
D  templates_volumes_old/julichbrain.txt
D  templates_volumes_old/lpba40.csv
D  templates_volumes_old/lpba40.nii
D  templates_volumes_old/lpba40.txt
D  templates_volumes_old/mori.csv
D  templates_volumes_old/mori.nii
D  templates_volumes_old/mori.txt
D  templates_volumes_old/neuromorphometrics.csv
D  templates_volumes_old/neuromorphometrics.nii
D  templates_volumes_old/neuromorphometrics.txt
D  templates_volumes_old/schaefer.txt
D  templates_volumes_old/templates.man

Deleted: Moved more files to new repository cat12-templates-atlases.
------------------------------------------------------------------------
r2442 | gaser | 2023-07-17 15:28:21

Changed paths:
 M .gitattributes
 M CHANGES.txt
 M templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.csv
 M templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.csv
 M templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.csv
 M templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.csv
 M templates_MNI152NLin2009cAsym/Tian_Subcortex_S4_7T.csv
 M templates_MNI152NLin2009cAsym/Tian_Subcortex_S4_7T.nii
 M templates_MNI152NLin2009cAsym/Tian_Subcortex_S4_7T.txt
 M templates_MNI152NLin2009cAsym/aal3.csv
 M templates_MNI152NLin2009cAsym/aal3.txt
 M templates_MNI152NLin2009cAsym/anatomy3.csv
 M templates_MNI152NLin2009cAsym/anatomy3.txt
 M templates_MNI152NLin2009cAsym/cat_bloodvessels.nii
 M templates_MNI152NLin2009cAsym/cobra.csv
 M templates_MNI152NLin2009cAsym/cobra.txt
 M templates_MNI152NLin2009cAsym/hammers.csv
 M templates_MNI152NLin2009cAsym/hammers.txt
 M templates_MNI152NLin2009cAsym/ibsr.csv
 M templates_MNI152NLin2009cAsym/ibsr.txt
 M templates_MNI152NLin2009cAsym/julichbrain.csv
 M templates_MNI152NLin2009cAsym/julichbrain.txt
 M templates_MNI152NLin2009cAsym/lpba40.csv
 M templates_MNI152NLin2009cAsym/lpba40.txt
 M templates_MNI152NLin2009cAsym/mori.csv
 M templates_MNI152NLin2009cAsym/mori.txt
 M templates_MNI152NLin2009cAsym/neuromorphometrics.csv
 M templates_MNI152NLin2009cAsym/neuromorphometrics.txt
 M templates_MNI152NLin2009cAsym/schaefer.txt
 M templates_MNI152NLin2009cAsym/suit.csv
 M templates_MNI152NLin2009cAsym/suit.txt
 M templates_MNI152NLin2009cAsym/templates.man
 M templates_MNI152NLin2009cAsym/thalamic_nuclei.csv
 M templates_MNI152NLin2009cAsym/thalamic_nuclei.txt
 M templates_MNI152NLin2009cAsym/thalamus.csv
 M templates_MNI152NLin2009cAsym/thalamus.txt

Changed: Reorganized LFS.
------------------------------------------------------------------------
r2441 | gaser | 2023-07-17 15:23:54

Changed paths:
 M .gitattributes
 M CHANGES.txt
D  atlases_surfaces_not_distributed/DKT40JT.txt
D  atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
D  atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
D  atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
D  atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
D  atlases_surfaces_not_distributed/lh.Schaefer2018_1000Parcels_17Networks_order.annot
D  atlases_surfaces_not_distributed/lh.Schaefer2018_1000Parcels_7Networks_order.annot
D  atlases_surfaces_not_distributed/lh.Schaefer2018_100Parcels_7Networks_order.annot
D  atlases_surfaces_not_distributed/lh.Schaefer2018_200Parcels_7Networks_order.annot
D  atlases_surfaces_not_distributed/lh.Schaefer2018_400Parcels_7Networks_order.annot
D  atlases_surfaces_not_distributed/lh.Schaefer2018_600Parcels_7Networks_order.annot
D  atlases_surfaces_not_distributed/lh.Schaefer2018_800Parcels_17Networks_order.annot
D  atlases_surfaces_not_distributed/lh.Schaefer2018_800Parcels_7Networks_order.annot
D  atlases_surfaces_not_distributed/lh.aal.Template_T1_IXI555_MNI152
D  atlases_surfaces_not_distributed/lh.aparc_DKT40JT.freesurfer.annot
D  atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
D  atlases_surfaces_not_distributed/lh.hammers.Template_T1_IXI555_MNI152
D  atlases_surfaces_not_distributed/lh.lpba40.Template_T1_IXI555_MNI152
D  atlases_surfaces_not_distributed/lh.mori.Template_T1_IXI555_MNI152
D  atlases_surfaces_not_distributed/lh.neuromorphometrics.Template_T1_IXI555_MNI152
D  atlases_surfaces_not_distributed/pals.txt
D  atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
D  atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
D  atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
D  atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
D  atlases_surfaces_not_distributed/rh.Schaefer2018_1000Parcels_17Networks_order.annot
D  atlases_surfaces_not_distributed/rh.Schaefer2018_1000Parcels_7Networks_order.annot
D  atlases_surfaces_not_distributed/rh.Schaefer2018_100Parcels_7Networks_order.annot
D  atlases_surfaces_not_distributed/rh.Schaefer2018_200Parcels_7Networks_order.annot
D  atlases_surfaces_not_distributed/rh.Schaefer2018_400Parcels_7Networks_order.annot
D  atlases_surfaces_not_distributed/rh.Schaefer2018_600Parcels_7Networks_order.annot
D  atlases_surfaces_not_distributed/rh.Schaefer2018_800Parcels_17Networks_order.annot
D  atlases_surfaces_not_distributed/rh.Schaefer2018_800Parcels_7Networks_order.annot
D  atlases_surfaces_not_distributed/rh.aal.Template_T1_IXI555_MNI152
D  atlases_surfaces_not_distributed/rh.aparc_DKT40JT.freesurfer.annot
D  atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
D  atlases_surfaces_not_distributed/rh.hammers.Template_T1_IXI555_MNI152
D  atlases_surfaces_not_distributed/rh.lpba40.Template_T1_IXI555_MNI152
D  atlases_surfaces_not_distributed/rh.mori.Template_T1_IXI555_MNI152
D  atlases_surfaces_not_distributed/rh.neuromorphometrics.Template_T1_IXI555_MNI152
D  templates_MNI152NLin2009cAsym_1mm/Template_0_GS1mm.nii
D  templates_MNI152NLin2009cAsym_1mm/Template_1_GS1mm.nii
D  templates_MNI152NLin2009cAsym_1mm/Template_2_GS1mm.nii
D  templates_MNI152NLin2009cAsym_1mm/Template_3_GS1mm.nii
D  templates_MNI152NLin2009cAsym_1mm/Template_4_GS1mm.nii
D  templates_MNI152NLin2009cSym/Template_0_GS.nii
D  templates_MNI152NLin2009cSym/Template_1_GS.nii
D  templates_MNI152NLin2009cSym/Template_2_GS.nii
D  templates_MNI152NLin2009cSym/Template_3_GS.nii
D  templates_MNI152NLin2009cSym/Template_4_GS.nii
D  templates_animals/ape_greater_T1.nii
D  templates_animals/ape_greater_T2.nii
D  templates_animals/ape_greater_TPM.nii
D  templates_animals/ape_greater_TPMt.nii
D  templates_animals/ape_greater_Template_1.nii
D  templates_animals/ape_greater_Template_2.nii
D  templates_animals/ape_greater_Template_3.nii
D  templates_animals/ape_greater_Template_4.nii
D  templates_animals/ape_greater_Template_5.nii
D  templates_animals/ape_greater_Template_6.nii
D  templates_animals/ape_greater_brainmask.nii
D  templates_animals/ape_greater_cat.nii
D  templates_animals/baboon_T1.nii
D  templates_animals/baboon_TPM.nii
D  templates_animals/baboon_Template_1.nii
D  templates_animals/baboon_Template_2.nii
D  templates_animals/baboon_Template_3.nii
D  templates_animals/baboon_Template_4.nii
D  templates_animals/baboon_Template_5.nii
D  templates_animals/baboon_Template_6.nii
D  templates_animals/baboon_brainmask.nii
D  templates_animals/baboon_cat.nii
D  templates_animals/chimpanzee_T1.nii
D  templates_animals/chimpanzee_TPM.nii
D  templates_animals/chimpanzee_Template_0_GS.nii
D  templates_animals/chimpanzee_Template_1_GS.nii
D  templates_animals/chimpanzee_Template_2_GS.nii
D  templates_animals/chimpanzee_Template_3_GS.nii
D  templates_animals/chimpanzee_Template_4_GS.nii
D  templates_animals/chimpanzee_atlas_davi.csv
D  templates_animals/chimpanzee_atlas_davi.nii
D  templates_animals/chimpanzee_atlas_davi.txt
D  templates_animals/chimpanzee_brainmask.nii
D  templates_animals/chimpanzee_cat.nii
D  templates_animals/dog_T1.nii
D  templates_animals/dog_Template_0.nii
D  templates_animals/dog_Template_1.nii
D  templates_animals/dog_Template_2.nii
D  templates_animals/dog_Template_3.nii
D  templates_animals/dog_Template_4.nii
D  templates_animals/dog_Template_5.nii
D  templates_animals/dog_Template_6.nii
D  templates_animals/dog_brainmask.nii
D  templates_animals/monkey_oldworld_T1.nii
D  templates_animals/monkey_oldworld_T2.nii
D  templates_animals/monkey_oldworld_TPM.nii
D  templates_animals/monkey_oldworld_Template_1.nii
D  templates_animals/monkey_oldworld_Template_2.nii
D  templates_animals/monkey_oldworld_Template_3.nii
D  templates_animals/monkey_oldworld_Template_4.nii
D  templates_animals/monkey_oldworld_Template_5.nii
D  templates_animals/monkey_oldworld_Template_6.nii
D  templates_animals/monkey_oldworld_atlas_inia19NeuroMaps.csv
D  templates_animals/monkey_oldworld_atlas_inia19NeuroMaps.nii
D  templates_animals/monkey_oldworld_atlas_inia19NeuroMaps.txt
D  templates_animals/monkey_oldworld_brainmask.nii
D  templates_animals/monkey_oldworld_cat.nii
D  templates_animals_surfaces/bh.headbrain.ape_greater_TPM.gii
D  templates_animals_surfaces/bh.headbrain.chimpanzee_TPM.gii
D  templates_animals_surfaces/bh.headbrain.monkey_oldworld_TPM.gii
D  templates_animals_surfaces/lc.central.Template_chimpanzee_T1_GS.gii
D  templates_animals_surfaces/lc.thickness.Template_chimpanzee_T1_GS
D  templates_animals_surfaces/lh.central.Template_chimpanzee_T1_GS.gii
D  templates_animals_surfaces/lh.thickness.Template_chimpanzee_T1_GS
D  templates_animals_surfaces/mesh.central.Template_chimpanzee_T1_GS.gii
D  templates_animals_surfaces/rc.central.Template_chimpanzee_T1_GS.gii
D  templates_animals_surfaces/rc.thickness.Template_chimpanzee_T1_GS
D  templates_animals_surfaces/rh.central.Template_chimpanzee_T1_GS.gii
D  templates_animals_surfaces/rh.thickness.Template_chimpanzee_T1_GS

Deleted: Moved unnecessary directories to new repository 
         cat12-templates-atlases.
------------------------------------------------------------------------
r2222 | gaser | 2023-07-17 13:49:56

Changed paths:
 M .gitattributes
 M CHANGES.txt
 M README.md
 M spm_cat12.m

Changed: Updated installation hints for Github version in README.md.
Fixed:   Corrected bug again in spm_cat12.m with missing definition of catdir.
------------------------------------------------------------------------
r2221 | gaser | 2023-07-17 12:49:02

Changed paths:
 M CHANGES.txt
 M README.md

Changed: Updated installation hints for Github version in README.md.
------------------------------------------------------------------------
r2220 | gaser | 2023-07-17 12:39:51

Changed paths:
 M CHANGES.txt
 M Contents.m
 M doc/cat.html
 M spm_cat12.m

Fixed: Corrected bug in spm_cat12.m with missing definition of catdir.

------------------------------------------------------------------------
r2219 | gaser | 2023-07-17 11:13:51

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_io_data2mat.m
 M cat_plot_boxplot.m
 M cat_surf_vol2surf.m
 M doc/cat.html

Changed: Some smaller edits in help text.
Fixed:   Corrected missing switch/case field in cat_surf_vol2surf.m.
------------------------------------------------------------------------
r2218 | rdahnke | 2023-07-10 17:49:53

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m
 M cat_io_cmd.m
 M cat_io_xml2csv.m
 M cat_main1639.m
 M cat_main_registration.m
 M cat_main_updateSPM1639.m
 M cat_parallelize.m
 M cat_surf_createCS3.m
 M cat_vol_mimcalc.m
 M cat_vol_partvol.m
 M cat_vol_qa2.m
 M cat_vol_set_com.m

1) Fixed:      Corrected setup of QC batch in cat_conf_tools and cat_vol_qa2.    
2) Fixed:      Tiny corrections/modifications in cat_io_cmd, cat_io_colormaps, 
               cat_main_updateSPM1639, cat_surf_createCS3, cat_vol_mimcalc.
3) Changed:    Modified ROI name limitation in cat_io_xml2csv.   
4) Changed:    Prepared new final affine registration after initial/final 
               segmentation in cat_main1639 and cat_main_registration.                 
5) Changed:    Shortened waiting times for PID in cat_parallelize.
4) Fixed:      Corrected matrix size bug of the brain mask in cat_vol_partvol. 
5) Changed:    Replaced mean by median threshold in cat_vol_set_com. 
------------------------------------------------------------------------
r2217 | rdahnke | 2023-06-21 17:13:14

Changed paths:
 M CHANGES.txt
 M cat_io_xml2csv.m

1) Fixed:    Added filename field and correct export directory bug in the 
             XML2CSV batch cat_io_xml2csv.
------------------------------------------------------------------------
r2216 | rdahnke | 2023-06-19 22:33:04

Changed paths:
 M CHANGES.txt
 M cat_conf_extopts.m
 M cat_surf_createCS3.m
 M cat_vol_pbt.m

Fixed:     Added suggestions from Torben Lund for expert surface outputs in
           cat_conf_extopts and . 
Changed:   Updated the cat_surf_createCS3 pipeline to reduce problems with blood
           Vessels. Removed the not working additional blood vessel correction. 
           Added SRP options to further improve reconstruction quality and added
           options in cat_conf_extopts. 
Changed:   Updated cat_vol_pbt and (i) removed old code (speedmap and filters), 
           and (ii) introduced a new filtering to reduce overestimations in the  
           initial thickness maps that caused ugly topology defects in the CS3
           pipeline.                
------------------------------------------------------------------------
r2215 | rdahnke | 2023-06-19 17:19:44

Changed paths:
 M CHANGES.txt
 M cat_main_amap.m
 M cat_main_amap1639.m
 M cat_main_cleanup.m
 M cat_main_updateSPM.m
 M cat_main_updateSPM1639.m
 M cat_run_job.m
 M cat_run_job1639.m

Fixed:     Improved more flexible detection of skull-stripped background in 
           cat_run_job1639 to support also non-zero values (required for some 
           simulated T1 images as the atrophy phantom in (Rusak et al., 2021). 
           cat_run_job is not compatible due to MP2Rage modification that has
           need further corrections later.  
           Extended background detections in cat_main_updateSPM1639.
Changed:   Corrected WMH class definition in cat_main_amap1639. 

------------------------------------------------------------------------
r2214 | rdahnke | 2023-06-19 15:30:34

Changed paths:
 M CHANGES.txt
 M cat_main.m
 M cat_main1639.m
 M cat_main_reportstr.m
 M cat_run.m
 M cat_vol_partvol.m
 M cat_vol_partvol1639.m

Changed:   Integrated new blood vessel correction into the old BVCstr parameter
           and updated the CAT report (cat_main_reportstr). The new BVC is only 
           used if required (cat_main#), i.e. many blood vessels with WM-like
           intensity were detected. Also included changes in cat_vol_partvol#. 
Changed:   Preparations for coming adaptions of the CS3 pipeline in cat_main#.          
Changed:   Deactivated cleanup corrections of the background in cat_main_cleanup
           that caused problems in the atrophy phantom and probably add also un-
           necessary variance in general (especially) longitudinal processing.                
Changed:   Extended waiting time for the creation of the log files in cat_run
           after observing some PID handling issues.              
Fixed:     Corrected setting of log-directory of the preprocessing in case of 
           BIDS in cat_run.        
Fixed:     Corrected stupid bug with spaces in main-log file name.    
------------------------------------------------------------------------
r2213 | gaser | 2023-06-19 10:32:44

Changed paths:
 M CHANGES.txt
 M cat_io_checkinopt.m
 M cat_io_updateStruct.m
 M cat_plot_scatter.m

Fixed:   Added missing value to "filled" option in cat_plot_scatter.m and check 
         whether X or Y have to be transposed.
------------------------------------------------------------------------
r2212 | rdahnke | 2023-06-09 14:10:08

Changed paths:
 M CHANGES.txt
 M cat_run.m
 M cat_surf_create_TPM_hull_surface.m
 M cat_vol_mp2rage.m

Changed:   Shortened waiting time for the creation of the log files in cat_run. 
Changed:   Changed bias-correction parameter setting in MP2Rage script. 
Fixed:     Corrected bug in cat_surf_create_hull_surface that prevent displaying
           of the mesh overlay in the CAT report.
------------------------------------------------------------------------
r2211 | rdahnke | 2023-06-02 22:08:11

Changed paths:
 M CHANGES.txt
 M cat_main1639.m
 M cat_vol_partvol1639.m

Changed:   Update blood vessel correction to reduce cutting of gyri with 
           extopts.experimental==1 (developer GUI). Tests showed better results
           for CS2 but still local problems for CS3.
------------------------------------------------------------------------
r2209 | rdahnke | 2023-05-26 15:00:52

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m
 M cat_vol_inpaint.m

Changed:   Update MP2Rage function cat_vol_mp2rage and batch in cat_conf_tools.
           Added help, bias correction, integrated SPM preprocessing, report, 
           batch file dependencies. 
Changed:   Added verbose setting (default=0 i.e. no progress bar) to  
           cat_vol_inpaint function.  
------------------------------------------------------------------------
r2208 | gaser | 2023-05-19 11:43:40

Changed paths:
 M CHANGES.txt
 M cat_vol_img2mip.m

Fixed: Added check to cat_vol_img2mip.m for empry results/images.
------------------------------------------------------------------------
r2207 | rdahnke | 2023-05-15 12:22:43

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m

New:     Added experimental function and batch to optimise MP2Rage data for CAT
         preprocessing.
------------------------------------------------------------------------
r2206 | gaser | 2023-05-11 12:08:58

Changed paths:
 M CHANGES.txt
 M cat_vol_eidist.m
AM cat_vol_inpaint.m
 M doc/index.html

Changed: Updated help text.
Added:   New function cat_vol_inpaint for inpainting of missing values.
------------------------------------------------------------------------
r2205 | rdahnke | 2023-05-08 09:34:57

Changed paths:
 M CHANGES.txt
 M cat_io_csv.m
 M cat_io_report.m
 M cat_main_reportfig.m

Fixed:   Corrected bug in cat_io_csv to read real NaNs.
Fixed:   Corrected bug in cat_io_report.   
Changed: Setup blood vessel output in cat_main_reportfig.
------------------------------------------------------------------------
r2201 | rdahnke | 2023-05-06 11:00:21

Changed paths:
 M CHANGES.txt

New:      Added min-max-based gray-scaled operations in cat_vol_morph.  
New:      Added new blood-vessel-detection in cat_vol_partvol1639 that 
          is controlled by the extopts.experimental parameter in the 
          developer mode.
Changed:  Optimized blood-vessel-correction in cat_main1639.  
------------------------------------------------------------------------
r2200 | gaser | 2023-05-04 16:48:07

Changed paths:
 M CHANGES.txt
 M cat_vol_tfce.m

Changed: Updated help text for cat_vol_tfce.m and set defaults for E and H.
------------------------------------------------------------------------
r2199 | gaser | 2023-05-04 13:52:45

Changed paths:
 M CHANGES.txt
 M Makefile
AM cat_vol_tfce.m
A  tfceMex_pthread.c
AM tfceMex_pthread.m
A  tfceMex_pthread.mexa64
A  tfceMex_pthread.mexmaca64
A  tfceMex_pthread.mexmaci64
A  tfceMex_pthread.mexw64

Added:   Added new function ca_vol_tfce.m that allows to apply threshold-free
         cluster enhancement (TFCE) and scale the image to have the same
         intensity distribution as the input.
Added:   Added tfceMex_pthread.* from TFCE toolbox.
------------------------------------------------------------------------
r2196 | gaser | 2023-05-02 23:37:42

Changed paths:
 M CHANGES.txt
 M cat_main_reportfig.m
 M cat_run_job1639.m
 M doc/index.html

Changed: Updated FAQ in CAT12 manual.
Fixed:   Corrected bug in cat_main_reportfig.m where the order of the temporary
         surfaces was wrong.
Fixed:   Corrected bug in cat_main_reportfig.m where the surface overlay was not
         working because the temporary surfaces were deleted too early.
------------------------------------------------------------------------
r2195 | rdahnke | 2023-05-02 14:55:45

Changed paths:
 M CHANGES.txt

Fixed:    Added missing files of previous update.
------------------------------------------------------------------------
r2194 | rdahnke | 2023-05-02 13:24:46

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m
 M cat_io_xml2csv.m
 M cat_stat_marks.m

Changed:    Extended quality evaluation batch in cat_conf_tools to support
            different qa-versions for experts.
Changed:    Updated cat_stat_marks to support different default scalings of
            different QA versions.
New:        Added cat_vol_qa2 that focuses on data preparation and evaluation
            to call different (older) QA versions.
New:        Added different versions of cat_vol_qa20* to support broader
            development and tests (that also include the ECR measure).

------------------------------------------------------------------------
r2193 | rdahnke | 2023-05-01 08:38:48

Changed paths:
 M CHANGES.txt
 M cat_io_addwarning.m
 M cat_io_lazy.m
 M cat_io_rerun.m
 M cat_plot_boxplot.m
 M cat_stat_kmeans.m
 M cat_surf_fun.m
 M cat_vol_grad.m
 M cat_vol_resize.m

Changed:    Added verbose flag to cat_io_addwarning.
Changed:    Improved verbose command line output of cat_io_lazy/rerun.
Changed:    Added (transparency) scatter plot (option) in cat_vol_boxplot.
Fixed:      Corrected small bugs of special cases in cat_vol_boxplot.
Fixed:      Small corrections of special cases in cat_stat_kmeans.
Fixed:      Corrected bug in cat_surf_fun.
Fixed:      Corrected bug in vx_vol access in cat_vol_resize.
Fixed:      Corrected definition of a special use case in cat_vol_grad.
------------------------------------------------------------------------
r2192 | rdahnke | 2023-04-29 16:43:17

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m
 M cat_io_struct2table.m
 M cat_io_xml2csv.m
 M cat_main_reportfig.m

Fixed:      Corrected bug of the just added boundary surface visualisation in
            cat_main_reportfig.
Changed:    Added option for verbose output and the sum progress bar in
            cat_io_struct2table.
New:        Added (new) XML2CSV export function and batch.
------------------------------------------------------------------------
r2190 | gaser | 2023-04-28 17:15:41

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_stat_homogeneity.m
 M cat_stat_quality_measures.m
 M doc/cat.html

Changed: Also changed the calculation to quartic mean Z-score for
         cat_stat_quality_measures.m
Fixed:   Corrected bug in cat_stat_homogeneity.m where defined report folder
         was not used for xml search.

------------------------------------------------------------------------
r2189 | rdahnke | 2023-04-28 11:33:47

Changed paths:
 M CHANGES.txt
 M cat_conf_extopts.m
 M cat_main_reportfig.m
 M cat_surf_create_TPM_hull_surface.m

Fixed:      Added CS3 pipeline in expert/developer GUI.
Fixed:      Correction of headbrain template surface settings in
            cat_surf_create_TPM_hull_surface.m
Changed:    Added overlay of white/pial surface in cat_main_reportfig.
------------------------------------------------------------------------
r2188 | rdahnke | 2023-04-27 16:19:04

Changed paths:
 M CHANGES.txt
AD batches/OASIS_bones_CT2MRI.m
AD bones_seg.m
 M cat_conf_tools.m
 M cat_io_mergeStruct.m
 M cat_io_updateStruct.m
 M cat_main.m
 M cat_main1639.m
 M cat_main_updateSPM.m
 M cat_main_updateSPM1639.m
 M cat_run.m
 M cat_run_job1639.m
AD templates_surfaces/bh.brain.human.TPM.gii
AD templates_surfaces/bh.headbrain.human.TPM.gii

Fixed:    Reactivated multi_subject_imcalc for developers in cat_conf_tools.
Fixed:    Corrections in cat_io_mergeStruct and cat_io_updateStruct.
Fixed:    Added CS3 surface pipeline case in cat_main.
Fixed:    Added missing variable for SPM-CAT pipeline in cat_main[1639].
Fixed:    Corrected fixed TPM loop number in cat_main_updateSPM1639.
Fixed:    Corrected typos in CHANGES.txt
Changed:  Be verbose in special longitudinal background model case in
          cat_run_job1639 (new_release only).
------------------------------------------------------------------------
r2186 | gaser | 2023-04-26 17:29:33

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m
 M cat_defaults.m
 M cat_spm_results_ui.m
 M cat_stat_homogeneity.m
 M doc/index.html

Changed: We now use quartic mean Z-score for sample homogeneity because outliers
         get a larger weight and are more obvious in the plot.
Changed: Updated help text in manual and cat_conf_tools for changes in sample
         homogeneity.
Fixed:   Corrected bug in cat_spm_results_ui.m that cause errors if analysis
         folder were moved.
------------------------------------------------------------------------
r2185 | gaser | 2023-04-17 10:23:42

Changed paths:
 M CHANGES.txt
 M cat_io_data2mat.m
 M cat_surf_createCS3.m
 M doc/index.html

Changed: Many changes to cat_io_data2mat.m to easier use it to prepare BrainAGE
         data and allow internal smoothing.
------------------------------------------------------------------------
r2184 | gaser | 2023-03-22 17:25:30

Changed paths:
 M CHANGES.txt
 M Contents.m
 M doc/cat.html
 M doc/index.html

Changed: Added more detailed description of WMH detection to manual.
------------------------------------------------------------------------
r2183 | gaser | 2023-03-17 15:19:17

Changed paths:
 M CAT.glnx86/CAT_3dVol2Surf
 M CAT.glnx86/CAT_AddValuesToSurf
 M CAT.glnx86/CAT_AverageSurfaces
 M CAT.glnx86/CAT_BlurSurfHK
 M CAT.glnx86/CAT_Central2Pial
 M CAT.glnx86/CAT_DeformSurf
 M CAT.glnx86/CAT_DumpCurv
 M CAT.glnx86/CAT_DumpSurfArea
 M CAT.glnx86/CAT_DumpSurfaceRatio
 M CAT.glnx86/CAT_FixTopology
 M CAT.glnx86/CAT_FractalDimension
 M CAT.glnx86/CAT_Hausdorff
 M CAT.glnx86/CAT_Isometize
 M CAT.glnx86/CAT_MarchingCubesGenus0
 M CAT.glnx86/CAT_MarkDefects
 M CAT.glnx86/CAT_RefineMesh
 M CAT.glnx86/CAT_ResampleSphericalSurf
 M CAT.glnx86/CAT_ResampleSphericalSurfSPH
 M CAT.glnx86/CAT_ResampleSurf
 M CAT.glnx86/CAT_SelfIntersect
 M CAT.glnx86/CAT_SeparatePolygon
 M CAT.glnx86/CAT_SmoothConvexity
 M CAT.glnx86/CAT_SulcusDepth
 M CAT.glnx86/CAT_Surf2Sphere
 M CAT.glnx86/CAT_Surf2Vol
 M CAT.glnx86/CAT_SurfDistance
 M CAT.glnx86/CAT_WarpSurf
 M CAT.maci64/CAT_3dVol2Surf
 M CAT.maci64/CAT_AddValuesToSurf
 M CAT.maci64/CAT_AverageSurfaces
 M CAT.maci64/CAT_BlurSurfHK
 M CAT.maci64/CAT_Central2Pial
 M CAT.maci64/CAT_DeformSurf
 M CAT.maci64/CAT_DumpCurv
 M CAT.maci64/CAT_DumpSurfArea
 M CAT.maci64/CAT_DumpSurfaceRatio
 M CAT.maci64/CAT_FixTopology
 M CAT.maci64/CAT_FractalDimension
 M CAT.maci64/CAT_Hausdorff
 M CAT.maci64/CAT_Isometize
M  CAT.maci64/CAT_MarchingCubesGenus0
 M CAT.maci64/CAT_MarkDefects
 M CAT.maci64/CAT_RefineMesh
 M CAT.maci64/CAT_ResampleSphericalSurf
 M CAT.maci64/CAT_ResampleSphericalSurfSPH
 M CAT.maci64/CAT_ResampleSurf
 M CAT.maci64/CAT_SelfIntersect
 M CAT.maci64/CAT_SeparatePolygon
 M CAT.maci64/CAT_SmoothConvexity
 M CAT.maci64/CAT_SulcusDepth
 M CAT.maci64/CAT_Surf2Sphere
 M CAT.maci64/CAT_Surf2Vol
 M CAT.maci64/CAT_SurfDistance
 M CAT.maci64/CAT_WarpSurf
 M CAT.w32/CAT_3dVol2Surf.exe
 M CAT.w32/CAT_AddValuesToSurf.exe
 M CAT.w32/CAT_AverageSurfaces.exe
 M CAT.w32/CAT_BlurSurfHK.exe
 M CAT.w32/CAT_Central2Pial.exe
 M CAT.w32/CAT_DeformSurf.exe
 M CAT.w32/CAT_DumpCurv.exe
 M CAT.w32/CAT_DumpSurfArea.exe
 M CAT.w32/CAT_DumpSurfaceRatio.exe
 M CAT.w32/CAT_FixTopology.exe
 M CAT.w32/CAT_FractalDimension.exe
 M CAT.w32/CAT_Hausdorff.exe
 M CAT.w32/CAT_Isometize.exe
 M CAT.w32/CAT_MarchingCubesGenus0.exe
 M CAT.w32/CAT_MarkDefects.exe
 M CAT.w32/CAT_RefineMesh.exe
 M CAT.w32/CAT_ResampleSphericalSurf.exe
 M CAT.w32/CAT_ResampleSphericalSurfSPH.exe
 M CAT.w32/CAT_ResampleSurf.exe
 M CAT.w32/CAT_SelfIntersect.exe
 M CAT.w32/CAT_SeparatePolygon.exe
 M CAT.w32/CAT_SmoothConvexity.exe
 M CAT.w32/CAT_SulcusDepth.exe
 M CAT.w32/CAT_Surf2Sphere.exe
 M CAT.w32/CAT_Surf2Vol.exe
 M CAT.w32/CAT_SurfDistance.exe
 M CAT.w32/CAT_WarpSurf.exe
 M CHANGES.txt

Changed: Updated CAT binaries.
------------------------------------------------------------------------
r2182 | gaser | 2023-03-14 16:13:41

Changed paths:
 M CHANGES.txt
A  cat_vol_sanlm2180.m

Added:   Renamed cat_vol_sanlm.m from r2180 to cat_vol_sanlm2180.m.
------------------------------------------------------------------------
r2181 | gaser | 2023-03-14 14:52:51

Changed paths:
 M CAT.glnx86/CAT_3dVol2Surf
 M CAT.glnx86/CAT_AddValuesToSurf
 M CAT.glnx86/CAT_AverageSurfaces
 M CAT.glnx86/CAT_BlurSurfHK
 M CAT.glnx86/CAT_Central2Pial
 M CAT.glnx86/CAT_DeformSurf
 M CAT.glnx86/CAT_DumpCurv
 M CAT.glnx86/CAT_DumpSurfArea
 M CAT.glnx86/CAT_DumpSurfaceRatio
 M CAT.glnx86/CAT_FixTopology
 M CAT.glnx86/CAT_FractalDimension
 M CAT.glnx86/CAT_Hausdorff
 M CAT.glnx86/CAT_Isometize
 M CAT.glnx86/CAT_MarchingCubesGenus0
 M CAT.glnx86/CAT_MarkDefects
 M CAT.glnx86/CAT_RefineMesh
 M CAT.glnx86/CAT_ResampleSphericalSurf
 M CAT.glnx86/CAT_ResampleSphericalSurfSPH
 M CAT.glnx86/CAT_ResampleSurf
 M CAT.glnx86/CAT_SelfIntersect
 M CAT.glnx86/CAT_SeparatePolygon
 M CAT.glnx86/CAT_SmoothConvexity
AD CAT.glnx86/CAT_SmoothDiffusion
 M CAT.glnx86/CAT_SulcusDepth
 M CAT.glnx86/CAT_Surf2Sphere
 M CAT.glnx86/CAT_Surf2Vol
 M CAT.glnx86/CAT_SurfDistance
 M CAT.glnx86/CAT_WarpSurf
 M CAT.maca64/CAT_3dVol2Surf
 M CAT.maca64/CAT_AddValuesToSurf
 M CAT.maca64/CAT_AverageSurfaces
 M CAT.maca64/CAT_BlurSurfHK
 M CAT.maca64/CAT_Central2Pial
 M CAT.maca64/CAT_DeformSurf
 M CAT.maca64/CAT_DumpCurv
 M CAT.maca64/CAT_DumpSurfArea
 M CAT.maca64/CAT_DumpSurfaceRatio
 M CAT.maca64/CAT_FixTopology
 M CAT.maca64/CAT_FractalDimension
 M CAT.maca64/CAT_Hausdorff
 M CAT.maca64/CAT_Isometize
 M CAT.maca64/CAT_MarchingCubesGenus0
 M CAT.maca64/CAT_MarkDefects
 M CAT.maca64/CAT_RefineMesh
 M CAT.maca64/CAT_ResampleSphericalSurf
 M CAT.maca64/CAT_ResampleSphericalSurfSPH
 M CAT.maca64/CAT_ResampleSurf
 M CAT.maca64/CAT_SelfIntersect
 M CAT.maca64/CAT_SeparatePolygon
 M CAT.maca64/CAT_SmoothConvexity
AD CAT.maca64/CAT_SmoothDiffusion
 M CAT.maca64/CAT_SulcusDepth
 M CAT.maca64/CAT_Surf2Sphere
 M CAT.maca64/CAT_Surf2Vol
 M CAT.maca64/CAT_SurfDistance
 M CAT.maca64/CAT_WarpSurf
 M CAT.maci64/CAT_3dVol2Surf
 M CAT.maci64/CAT_AddValuesToSurf
 M CAT.maci64/CAT_AverageSurfaces
 M CAT.maci64/CAT_BlurSurfHK
 M CAT.maci64/CAT_Central2Pial
 M CAT.maci64/CAT_DeformSurf
 M CAT.maci64/CAT_DumpCurv
 M CAT.maci64/CAT_DumpSurfArea
 M CAT.maci64/CAT_DumpSurfaceRatio
 M CAT.maci64/CAT_FixTopology
 M CAT.maci64/CAT_FractalDimension
 M CAT.maci64/CAT_Hausdorff
 M CAT.maci64/CAT_Isometize
 M CAT.maci64/CAT_MarchingCubesGenus0
 M CAT.maci64/CAT_MarkDefects
 M CAT.maci64/CAT_RefineMesh
 M CAT.maci64/CAT_ResampleSphericalSurf
 M CAT.maci64/CAT_ResampleSphericalSurfSPH
 M CAT.maci64/CAT_ResampleSurf
 M CAT.maci64/CAT_SelfIntersect
 M CAT.maci64/CAT_SeparatePolygon
 M CAT.maci64/CAT_SmoothConvexity
AD CAT.maci64/CAT_SmoothDiffusion
 M CAT.maci64/CAT_SulcusDepth
 M CAT.maci64/CAT_Surf2Sphere
 M CAT.maci64/CAT_Surf2Vol
 M CAT.maci64/CAT_SurfDistance
 M CAT.maci64/CAT_WarpSurf
 M CAT.w32/CAT_3dVol2Surf.exe
 M CAT.w32/CAT_AddValuesToSurf.exe
 M CAT.w32/CAT_AverageSurfaces.exe
 M CAT.w32/CAT_BlurSurfHK.exe
 M CAT.w32/CAT_Central2Pial.exe
 M CAT.w32/CAT_DeformSurf.exe
 M CAT.w32/CAT_DumpCurv.exe
 M CAT.w32/CAT_DumpSurfArea.exe
 M CAT.w32/CAT_DumpSurfaceRatio.exe
 M CAT.w32/CAT_FixTopology.exe
 M CAT.w32/CAT_FractalDimension.exe
 M CAT.w32/CAT_Hausdorff.exe
 M CAT.w32/CAT_Isometize.exe
 M CAT.w32/CAT_MarchingCubesGenus0.exe
 M CAT.w32/CAT_MarkDefects.exe
 M CAT.w32/CAT_RefineMesh.exe
 M CAT.w32/CAT_ResampleSphericalSurf.exe
 M CAT.w32/CAT_ResampleSphericalSurfSPH.exe
 M CAT.w32/CAT_ResampleSurf.exe
 M CAT.w32/CAT_SelfIntersect.exe
 M CAT.w32/CAT_SeparatePolygon.exe
 M CAT.w32/CAT_SmoothConvexity.exe
AD CAT.w32/CAT_SmoothDiffusion.exe
 M CAT.w32/CAT_SulcusDepth.exe
 M CAT.w32/CAT_Surf2Sphere.exe
 M CAT.w32/CAT_Surf2Vol.exe
 M CAT.w32/CAT_SurfDistance.exe
 M CAT.w32/CAT_WarpSurf.exe
 M CHANGES.txt
 M Contents.m
 M cat_defaults.m
 M cat_long_main.m
 M cat_long_multi_run.m
 M cat_main1639.m
 M cat_main_amap1639.m
 M cat_main_reportstr.m
 M cat_main_updateSPM1639.m
 M cat_stat_analyze_ROIs.m
 M cat_surf_createCS2.m
 M cat_surf_createCS3.m
 M cat_surf_create_TPM_hull_surface.m
 M cat_surf_surf2roi.m
 M cat_vol_morph.m
 M cat_vol_sanlm.m
 M check_pipeline.sh
 M doc/cat.html
 M templates_MNI152NLin2009cAsym/Tian_Subcortex_S4_7T.nii

Changed: Rescued old cat_vol_sanlm from r1980 that worked much better and
         renamed current version to cat_vol_sanlm2180.m.
Changed: Updated CAT binaries to newer version.
Changed: Set new CS3 surface pipeline as default.
Changed: Added flag for filtering avg images with SANLM to cat_long_main.m.
Changed: Many changes to new CS3 surface pipeline that now additionally uses
         brainmask from gcut.
Changed: Suppress output of surface parameters in cat_main_reportfig.m if values
         are not defined (i.e. for new CS3 pipeline).
Changed: Disabled isMP2RAGE flag in cat_main_updateSPM1639.m that worked not
         correct.
Changed: Removed progress bar from cat_surf_surf2roi.m.
Fixed:   Corrected bug in cat_vol_morph.m where the lab-option was not always
         considered correctly.
Fixed:   Corrected orientation of Tians Subcortical atlas.
------------------------------------------------------------------------
r2180 | gaser | 2023-02-24 16:44:28

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_defaults.m
 M cat_main.m
 M cat_main1639.m
 M cat_plot_circular.m
 M cat_progress_bar.m
 M cat_stat_check_cov_old.m
 M cat_stat_homogeneity.m
 M cat_stat_quality_measures.m
AM cat_surf_createCS3.m
 M cat_vol_morph.m
 M check_pipeline.sh
 M doc/cat.html
 M templates_MNI152NLin2009cAsym/neuromorphometrics.csv

Changed: Prepared calls to new CS3 surface pipeline in many functions.
Changed: Updated help text for cat_plot_circular.m.
Changed: Replaced try/catch calls in cat_progress_bar by check for image handle.
Changed: Added checks for EC_abs and defect_size parameter to consider new CS3
         surface pipeline that is not providing these values anymore.
Changed: Added some more fields for circular plots to neuromorphometrics atlas.
Added:   New Surface pipeline cat_surf_createCS3.m that uses volume-based
         topology correction that prevents many issues in surface processing and
         also uses adaptive vdist that controls mesh resolution w.r.t. spatial
         resolution of the input images.
------------------------------------------------------------------------
r2179 | gaser | 2023-02-17 10:34:34

Changed paths:
 M CAT.glnx86/CAT_3dVol2Surf
 M CAT.glnx86/CAT_AddValuesToSurf
 M CAT.glnx86/CAT_AverageSurfaces
 M CAT.glnx86/CAT_BlurSurfHK
 M CAT.glnx86/CAT_Central2Pial
 M CAT.glnx86/CAT_DeformSurf
 M CAT.glnx86/CAT_DumpCurv
 M CAT.glnx86/CAT_DumpSurfArea
 M CAT.glnx86/CAT_DumpSurfaceRatio
 M CAT.glnx86/CAT_FixTopology
 M CAT.glnx86/CAT_FractalDimension
 M CAT.glnx86/CAT_Hausdorff
 M CAT.glnx86/CAT_Isometize
 M CAT.glnx86/CAT_MarchingCubesGenus0
 M CAT.glnx86/CAT_MarkDefects
 M CAT.glnx86/CAT_RefineMesh
 M CAT.glnx86/CAT_ResampleSphericalSurf
 M CAT.glnx86/CAT_ResampleSphericalSurfSPH
 M CAT.glnx86/CAT_ResampleSurf
 M CAT.glnx86/CAT_SelfIntersect
 M CAT.glnx86/CAT_SeparatePolygon
 M CAT.glnx86/CAT_SmoothConvexity
 M CAT.glnx86/CAT_SulcusDepth
 M CAT.glnx86/CAT_Surf2Sphere
 M CAT.glnx86/CAT_Surf2Vol
 M CAT.glnx86/CAT_SurfDistance
 M CAT.glnx86/CAT_WarpSurf
 M CAT.maca64/CAT_3dVol2Surf
 M CAT.maca64/CAT_AddValuesToSurf
 M CAT.maca64/CAT_AverageSurfaces
 M CAT.maca64/CAT_BlurSurfHK
 M CAT.maca64/CAT_Central2Pial
 M CAT.maca64/CAT_DeformSurf
 M CAT.maca64/CAT_DumpCurv
 M CAT.maca64/CAT_DumpSurfArea
 M CAT.maca64/CAT_DumpSurfaceRatio
 M CAT.maca64/CAT_FixTopology
 M CAT.maca64/CAT_FractalDimension
 M CAT.maca64/CAT_Hausdorff
 M CAT.maca64/CAT_Isometize
 M CAT.maca64/CAT_MarchingCubesGenus0
 M CAT.maca64/CAT_MarkDefects
 M CAT.maca64/CAT_RefineMesh
 M CAT.maca64/CAT_ResampleSphericalSurf
 M CAT.maca64/CAT_ResampleSphericalSurfSPH
 M CAT.maca64/CAT_ResampleSurf
 M CAT.maca64/CAT_SelfIntersect
 M CAT.maca64/CAT_SeparatePolygon
 M CAT.maca64/CAT_SmoothConvexity
 M CAT.maca64/CAT_SulcusDepth
 M CAT.maca64/CAT_Surf2Sphere
 M CAT.maca64/CAT_Surf2Vol
 M CAT.maca64/CAT_SurfDistance
 M CAT.maca64/CAT_WarpSurf
 M CAT.maci64/CAT_3dVol2Surf
 M CAT.maci64/CAT_AddValuesToSurf
 M CAT.maci64/CAT_AverageSurfaces
 M CAT.maci64/CAT_BlurSurfHK
 M CAT.maci64/CAT_Central2Pial
 M CAT.maci64/CAT_DeformSurf
 M CAT.maci64/CAT_DumpCurv
 M CAT.maci64/CAT_DumpSurfArea
 M CAT.maci64/CAT_DumpSurfaceRatio
 M CAT.maci64/CAT_FixTopology
 M CAT.maci64/CAT_FractalDimension
 M CAT.maci64/CAT_Hausdorff
 M CAT.maci64/CAT_Isometize
 M CAT.maci64/CAT_MarchingCubesGenus0
 M CAT.maci64/CAT_MarkDefects
 M CAT.maci64/CAT_RefineMesh
 M CAT.maci64/CAT_ResampleSphericalSurf
 M CAT.maci64/CAT_ResampleSphericalSurfSPH
 M CAT.maci64/CAT_ResampleSurf
 M CAT.maci64/CAT_SelfIntersect
 M CAT.maci64/CAT_SeparatePolygon
 M CAT.maci64/CAT_SmoothConvexity
 M CAT.maci64/CAT_SulcusDepth
 M CAT.maci64/CAT_Surf2Sphere
 M CAT.maci64/CAT_Surf2Vol
 M CAT.maci64/CAT_SurfDistance
 M CAT.maci64/CAT_WarpSurf
 M CAT.w32/CAT_3dVol2Surf.exe
 M CAT.w32/CAT_AddValuesToSurf.exe
 M CAT.w32/CAT_AverageSurfaces.exe
 M CAT.w32/CAT_BlurSurfHK.exe
 M CAT.w32/CAT_Central2Pial.exe
 M CAT.w32/CAT_DeformSurf.exe
 M CAT.w32/CAT_DumpCurv.exe
 M CAT.w32/CAT_DumpSurfArea.exe
 M CAT.w32/CAT_DumpSurfaceRatio.exe
 M CAT.w32/CAT_FixTopology.exe
 M CAT.w32/CAT_FractalDimension.exe
 M CAT.w32/CAT_Hausdorff.exe
 M CAT.w32/CAT_Isometize.exe
 M CAT.w32/CAT_MarchingCubesGenus0.exe
 M CAT.w32/CAT_MarkDefects.exe
 M CAT.w32/CAT_RefineMesh.exe
 M CAT.w32/CAT_ResampleSphericalSurf.exe
 M CAT.w32/CAT_ResampleSphericalSurfSPH.exe
 M CAT.w32/CAT_ResampleSurf.exe
 M CAT.w32/CAT_SelfIntersect.exe
 M CAT.w32/CAT_SeparatePolygon.exe
 M CAT.w32/CAT_SmoothConvexity.exe
 M CAT.w32/CAT_SulcusDepth.exe
 M CAT.w32/CAT_Surf2Sphere.exe
 M CAT.w32/CAT_Surf2Vol.exe
 M CAT.w32/CAT_SurfDistance.exe
 M CAT.w32/CAT_WarpSurf.exe
 M CHANGES.txt
 M cat_main1639.m
 M cat_progress_bar.m
 M doc/index.html

Changed: Updated CAT-binaries.
Changed: Added FAQ section to online manual.
Changed: Added try/catch call to cat_progress_bar in case that progress window
         is closed by user.
Fixed:   Corrected try/catch call in cat_main1639.m.
------------------------------------------------------------------------
r2177 | gaser | 2023-02-09 17:14:05

Changed paths:
A  CAT.glnx86/CAT_MarchingCubesGenus0
A  CAT.maca64/CAT_MarchingCubesGenus0
A  CAT.maci64/CAT_MarchingCubesGenus0
A  CAT.w32/CAT_MarchingCubesGenus0.exe
 M CHANGES.txt

Changed: Updated CAT-binaries and added new Marching Cubes method.
Changed: Added support for Apple ARM64 to Makefile.
------------------------------------------------------------------------
r2176 | gaser | 2023-02-09 17:11:51

Changed paths:
 M CAT.glnx86/CAT_3dVol2Surf
 M CAT.glnx86/CAT_AddValuesToSurf
 M CAT.glnx86/CAT_AverageSurfaces
 M CAT.glnx86/CAT_BlurSurfHK
 M CAT.glnx86/CAT_Central2Pial
 M CAT.glnx86/CAT_DeformSurf
 M CAT.glnx86/CAT_DumpCurv
 M CAT.glnx86/CAT_DumpSurfArea
 M CAT.glnx86/CAT_DumpSurfaceRatio
 M CAT.glnx86/CAT_FixTopology
 M CAT.glnx86/CAT_FractalDimension
 M CAT.glnx86/CAT_Hausdorff
 M CAT.glnx86/CAT_Isometize
 M CAT.glnx86/CAT_MarkDefects
 M CAT.glnx86/CAT_RefineMesh
 M CAT.glnx86/CAT_ResampleSphericalSurf
 M CAT.glnx86/CAT_ResampleSphericalSurfSPH
 M CAT.glnx86/CAT_ResampleSurf
 M CAT.glnx86/CAT_SelfIntersect
 M CAT.glnx86/CAT_SeparatePolygon
 M CAT.glnx86/CAT_SmoothConvexity
 M CAT.glnx86/CAT_SulcusDepth
 M CAT.glnx86/CAT_Surf2Sphere
 M CAT.glnx86/CAT_Surf2Vol
 M CAT.glnx86/CAT_SurfDistance
 M CAT.glnx86/CAT_WarpSurf
 M CAT.maca64/CAT_3dVol2Surf
 M CAT.maca64/CAT_AddValuesToSurf
 M CAT.maca64/CAT_AverageSurfaces
 M CAT.maca64/CAT_BlurSurfHK
 M CAT.maca64/CAT_Central2Pial
 M CAT.maca64/CAT_DeformSurf
 M CAT.maca64/CAT_DumpCurv
 M CAT.maca64/CAT_DumpSurfArea
 M CAT.maca64/CAT_DumpSurfaceRatio
 M CAT.maca64/CAT_FixTopology
 M CAT.maca64/CAT_FractalDimension
 M CAT.maca64/CAT_Hausdorff
 M CAT.maca64/CAT_Isometize
 M CAT.maca64/CAT_MarkDefects
 M CAT.maca64/CAT_RefineMesh
 M CAT.maca64/CAT_ResampleSphericalSurf
 M CAT.maca64/CAT_ResampleSphericalSurfSPH
 M CAT.maca64/CAT_ResampleSurf
 M CAT.maca64/CAT_SelfIntersect
 M CAT.maca64/CAT_SeparatePolygon
 M CAT.maca64/CAT_SmoothConvexity
 M CAT.maca64/CAT_SulcusDepth
 M CAT.maca64/CAT_Surf2Sphere
 M CAT.maca64/CAT_Surf2Vol
 M CAT.maca64/CAT_SurfDistance
 M CAT.maca64/CAT_WarpSurf
 M CAT.maci64/CAT_3dVol2Surf
 M CAT.maci64/CAT_AddValuesToSurf
 M CAT.maci64/CAT_AverageSurfaces
 M CAT.maci64/CAT_BlurSurfHK
 M CAT.maci64/CAT_Central2Pial
 M CAT.maci64/CAT_DeformSurf
 M CAT.maci64/CAT_DumpCurv
 M CAT.maci64/CAT_DumpSurfArea
 M CAT.maci64/CAT_DumpSurfaceRatio
 M CAT.maci64/CAT_FixTopology
 M CAT.maci64/CAT_FractalDimension
 M CAT.maci64/CAT_Hausdorff
 M CAT.maci64/CAT_Isometize
 M CAT.maci64/CAT_MarkDefects
 M CAT.maci64/CAT_RefineMesh
 M CAT.maci64/CAT_ResampleSphericalSurf
 M CAT.maci64/CAT_ResampleSphericalSurfSPH
 M CAT.maci64/CAT_ResampleSurf
 M CAT.maci64/CAT_SelfIntersect
 M CAT.maci64/CAT_SeparatePolygon
 M CAT.maci64/CAT_SmoothConvexity
 M CAT.maci64/CAT_SulcusDepth
 M CAT.maci64/CAT_Surf2Sphere
 M CAT.maci64/CAT_Surf2Vol
 M CAT.maci64/CAT_SurfDistance
 M CAT.maci64/CAT_WarpSurf
 M CAT.w32/CAT_3dVol2Surf.exe
 M CAT.w32/CAT_AddValuesToSurf.exe
 M CAT.w32/CAT_AverageSurfaces.exe
 M CAT.w32/CAT_BlurSurfHK.exe
 M CAT.w32/CAT_Central2Pial.exe
 M CAT.w32/CAT_DeformSurf.exe
 M CAT.w32/CAT_DumpCurv.exe
 M CAT.w32/CAT_DumpSurfArea.exe
 M CAT.w32/CAT_DumpSurfaceRatio.exe
 M CAT.w32/CAT_FixTopology.exe
 M CAT.w32/CAT_FractalDimension.exe
 M CAT.w32/CAT_Hausdorff.exe
 M CAT.w32/CAT_Isometize.exe
 M CAT.w32/CAT_MarkDefects.exe
 M CAT.w32/CAT_RefineMesh.exe
 M CAT.w32/CAT_ResampleSphericalSurf.exe
 M CAT.w32/CAT_ResampleSphericalSurfSPH.exe
 M CAT.w32/CAT_ResampleSurf.exe
 M CAT.w32/CAT_SelfIntersect.exe
 M CAT.w32/CAT_SeparatePolygon.exe
 M CAT.w32/CAT_SmoothConvexity.exe
 M CAT.w32/CAT_SulcusDepth.exe
 M CAT.w32/CAT_Surf2Sphere.exe
 M CAT.w32/CAT_Surf2Vol.exe
 M CAT.w32/CAT_SurfDistance.exe
 M CAT.w32/CAT_WarpSurf.exe
 M CHANGES.txt
 M Makefile
 M cat_surf_createCS2.m

Changed: Updated CAT-binaries and added new Marching Cubes method.
Changed: Added support for Apple ARM64 to Makefile.
------------------------------------------------------------------------
r2175 | gaser | 2023-02-03 08:47:50

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_surf_results.m
 M cat_vol_glassbrain.m
 M doc/cat.html
 M doc/index.html

Changed: Updated online documentation.
Changed: Updated roi option in cat_vol_glassbrain.m and calls in
         call_surf_results.m.
------------------------------------------------------------------------
r2174 | gaser | 2023-01-31 15:41:18

Changed paths:
 M CHANGES.txt
 M Makefile
 M cat_main1639.m
 M cat_stat_confplot_spm.m
 M cat_vol_glassbrain.m
 M cat_vol_img2mip.m

Changed: Added again release information to standalone version in Makefile.
Changed: Added scatter density plot to cat_stat_confplot_spm.m.
Changed: Added new roi option to cat_vol_img2mip.m and opportunity to provide
         nifti structure as input to prevent loading files.
Changed: New roi flag for overlaying ROI#s onto MIP view.
Fixed:   Check for 'stable' option for unique command in cat_main1639.m.
------------------------------------------------------------------------
r2173 | gaser | 2023-01-30 09:33:25

Changed paths:
 M CHANGES.txt
 M cat_check.m
 M cat_run_job1639.m
 M cat_vol_glassbrain.m
 M cat_vol_morph.m
 M spm_cat12.m

Changed: Added flag to cat_vol_glassbrain.m to control (symmetrical) range of
         colorbar.
Changed: Updated some more functions to run under Octave.
Fixed:   Corrected handling of lab function in cat_vol_morph.m and removed
         subfunction that was not used anymore.
------------------------------------------------------------------------
r2172 | gaser | 2023-01-28 21:40:16

Changed paths:
 M CHANGES.txt
 M README.md
 M cat_update.m
 M doc/index.html

Changed: Updated information about standalone versions ins Readme.md.
Changed: Added option to download only to cat_update.m.
------------------------------------------------------------------------
r2171 | gaser | 2023-01-27 13:13:31

Changed paths:
 M CHANGES.txt
 M Contents.m
 M Makefile
 M cat_run.m
 M doc/cat.html
 D git_ci_log

Changed: Updated Makefile for Octave installation.
Fixed:   Shooting caused issues on Octave and I had to set back the limitation
         to Dartel for Octave use.
------------------------------------------------------------------------
r2170 | gaser | 2023-01-26 17:32:29

Changed paths:
 M CHANGES.txt
 M cat_vol_display_label.m
 M doc/index.html
 M templates_MNI152NLin2009cAsym/Tian_Subcortex_S4_7T.csv

Changed: Updated and corrected atlas information for new subcortical atlas in
         csv file and online documentation.
Changed: Added check to cat_vol_display_label.m if new atlases were not yet
         installed.
------------------------------------------------------------------------
r2169 | gaser | 2023-01-26 14:34:04

Changed paths:
 M CHANGES.txt
 M Contents.m
A  cat_vol_addtruecolourimage.m
 M doc/cat.html
 M doc/index.html

Added:   Added function to overlay 2..12 images either as multiple overlay or
         as RGB overlay for up to 3 images.
Changed: Added link to new subcortical atlas.
------------------------------------------------------------------------
r2168 | gaser | 2023-01-26 09:51:10

Changed paths:
 M .gitattributes
 M CHANGES.txt
 M cat_defaults.m
 M cat_vol_glassbrain.m
 M cat_vol_img2mip.m
 M doc/index.html
A  templates_MNI152NLin2009cAsym/Tian_Subcortex_S4_7T.csv
A  templates_MNI152NLin2009cAsym/Tian_Subcortex_S4_7T.nii
A  templates_MNI152NLin2009cAsym/Tian_Subcortex_S4_7T.txt
 M templates_MNI152NLin2009cAsym/templates.man
 M templates_MNI152NLin2009cAsym_1mm/Template_0_GS1mm.nii
 M templates_MNI152NLin2009cAsym_1mm/Template_1_GS1mm.nii
 M templates_MNI152NLin2009cAsym_1mm/Template_2_GS1mm.nii
 M templates_MNI152NLin2009cAsym_1mm/Template_3_GS1mm.nii
 M templates_MNI152NLin2009cAsym_1mm/Template_4_GS1mm.nii

Added:   Added new subcortical atlas bi Tian et al.
Changed: Updated cat_defaults.m and online documentation to consider new atlas.
Changed: Added slight position corrections to cat_vol_glassbrain.m and
         cat_vol_img2mip.m to better fit MNI152NLin2009cAsym atlas to the
         saved MIPs.
Fixed:   Corrected 1mm GS template in x-axis by -0.5mm because of small
         discrepancies to the 1.5mm atlas.
------------------------------------------------------------------------
r2167 | gaser | 2023-01-23 10:49:36

Changed paths:
 M CHANGES.txt
 M Contents.m
 M Makefile
 M doc/cat.html
 M doc/index.html

Changed: Updated Makefile to add tag.
------------------------------------------------------------------------
r2166 | gaser | 2023-01-22 23:40:08

Changed paths:
 M CHANGES.txt
 M cat_io_cprintf.m
 M cat_io_xml.m
 M cat_main_reportfig.m
 M cat_main_reportstr.m
 M cat_main_updateSPM1639.m
 M cat_run.m
 M cat_spm_results_ui.m
 M cat_stat_check_cov_old.m
 M cat_surf_createCS2.m
 M cat_surf_results.m
 M cat_vbdist.c
 M cat_vol_approx.m
 M cat_vol_slice_overlay.m
 M compile.m
 M spm_cat12.m

Changed: Made many changes for octave compatibility.
Fixed:   Corrected wrong arguments in sprintf command in
         cat_main_updateSPM1639.m
Fixed:   Contrasts were sometimes not recognized in cat_spm_results_ui.m because
         we have to go into the analysis folder.
Fixed:   Clipping should be ignored for cat_vol_slice_overlay if lower and upper
         clipping values are equal.
Fixed:   Figure in cat_vol_slice_overlay_ui.m was set to invisible.
------------------------------------------------------------------------
r2164 | gaser | 2023-01-14 21:46:06

Changed paths:
 M CHANGES.txt
 M cat_stat_check_SPM.m
 M doc/index.html

Changed: Updated CAT12 online manual (Orthogonalization).
Fixed:   Corrected error in cat_stat_check_SPM.m where the check for
         orthogonality was not correct recognised.
------------------------------------------------------------------------
r2163 | gaser | 2023-01-12 17:59:59

Changed paths:
 M Amap.c
 M CHANGES.txt
 M cat_main_cleanup.m
 M sanlm_float.c

Changed: Some tiny edits in text formatting.
------------------------------------------------------------------------
r2162 | gaser | 2022-12-27 17:00:50

Changed paths:
 M CHANGES.txt
 M cat12.m
 M cat_conf_extopts.m
 M cat_conf_factorial.m
 M cat_conf_tools.m
 M cat_parallelize.m
 M cat_run.m
 M cat_stat_spm2x.m
 M cat_surf_parameters.m
 M cat_surf_resamp.m
 M doc/index.html
 M git_ci_log

Changed: Added again option for registration method for support use of
         customised templates in cat_conf_extopts.m.
Changed: Added file filter for meshes in cat_conf_factorial.m to only allow
         selecting resampled data.
Changed: Shortened time between paralellized processes to 2s to get rid of the
         long waiting time for most processes, but recognise if long.
         segmentation is used and use 30s.
Changed: Removed some old calls in cat_run.m that are not used anymore.
Changed: Updated help function for cat_surf_parameters.m.
Changed: Replaced try/catch by file checking in cat_surf_resamp.m.
------------------------------------------------------------------------
r2161 | gaser | 2022-12-09 10:26:13

Changed paths:
 M CHANGES.txt
 M Makefile
 M cat_batch_cat.sh
 M cat_batch_spm.sh


Changed: Added fg flag to cat_batch_spm.sh and changed call to always use
         nohup.
------------------------------------------------------------------------
r2160 | gaser | 2022-12-08 14:12:11

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_conf_factorial.m
 M cat_surf_results.m
 M cat_vol_slice_overlay.m
 M cat_vol_slice_overlay_ui.m
 M doc/cat.html


Changed: Added new clip flag to cat_vol_slice_overlay that replaces the func
         flag and allows to create colorbar that is gray for values below
         the threshold.
Changed: Updated cat_surf_results to use new clipping flag for volumes.
Fixed:   Corrected check for fields for voxel-wise covariates in
         cat_conf_factorial.m
------------------------------------------------------------------------
r2159 | gaser | 2022-12-07 15:18:51

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_conf_factorial.m
 M cat_conf_stools.m
 M doc/cat.html
 M doc/index.html


Changed: Updated help text in cat_conf_stools.m.
Fixed:   Corrected file selection in cat_conf_factorial.m that hided meshes.
------------------------------------------------------------------------
r2158 | rdahnke | 2022-12-03 14:14:35

Changed paths:
 M CHANGES.txt
A  cat_main_report.m


New:    Added cat_main_report?
------------------------------------------------------------------------
r2157 | rdahnke | 2022-12-03 14:10:57

Changed paths:
 M CHANGES.txt


New:    Added cat_main_report?
------------------------------------------------------------------------
r2156 | rdahnke | 2022-12-03 14:08:53

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m


Fixed:    Small corrections on the CAT report batch.
------------------------------------------------------------------------
r2155 | gaser | 2022-12-02 16:37:30

Changed paths:
 M CHANGES.txt


Changed: Added contrast field to cat_conf_factorial to define contrasts for
         voxel-wise covariate.
Fixed:   Corrected fieldnames in cat_stat_check_SPM that were different.
------------------------------------------------------------------------
r2152 | rdahnke | 2022-12-02 12:53:43

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m
 M cat_main1639.m
 M cat_main_reportfig.m
 M cat_main_reportstr.m
 M cat_surf_info.m
 M cat_surf_rename.m
 M cat_surf_render2.m


New:     Added matlabbatch cat_main_report for retrospective creation of CAT
         reports based on the XML file in cat_conf_tools.
Changed: Small addaptations to use cat_main_reportstr, cat_main_reportfig,
         cat_surf_render2, cat_surf_info and cat_surf_rename
         for the retrospective report generation.
------------------------------------------------------------------------
r2151 | gaser | 2022-12-01 11:35:59

Changed paths:
 M CHANGES.txt
 M cat_stat_check_SPM.m
 M cat_stat_homogeneity.m


Changed: Removed some unnecessary lines in cat_stat_check_SPM.m.
Changed: Added check for longitudinal designs if design matrix is not given as
         argument in job parameter to cat_stat_homogeneity.m.
------------------------------------------------------------------------
r2150 | gaser | 2022-12-01 10:59:13

Changed paths:
 M CHANGES.txt
 M Contents.m
 M Makefile
 M cat12.m
 M cat_stat_check_SPM.m
 M cat_stat_homogeneity.m
 M cat_surf_results.m
 M cat_system.m
 M cat_vol_groupwise_ls.m
AD cat_vol_groupwise_ls_orig.m
 M cat_vol_img2mip.m
 M check_pipeline.sh
 M check_pipeline_homogeneity.m
 M doc/cat.html
 M doc/index.html
A  spm_diffeo.mexa64
A  spm_diffeo.mexmaca64
A  spm_diffeo.mexmaci64
A  spm_diffeo.mexw32
A  spm_diffeo.mexw64
AD spm_diffeo_old.m


Added:   New maca64-compiled mex-files.
Changed: cat_vol_groupwise_ls.m is now using the newer version of SPM_diffeo
         that is now also provided with CAT12.
Changed: Added flag to define Matlab version in check_pipeline.sh.
Fixed:   Corrected call to new homogeneity tool in check_pipeline_homogeneity.m.
Fixed:   Printed RGB colors in cat_vol_img2mip.m are now correct.
Fixed:   Some markers for the scatterplot in cat_stat_homogeneity were not
         allowed for all Matlab versions.
Fixed:   Call of cat_stat_check_SPM from CAT12 GUI was not correct.
Fixed:   Corrected use of different parameter fields in of cat_stat_check_SPM.m.
Fixed:   Corrected some smaller issues with filenames in cat_surf_results.m.
------------------------------------------------------------------------
r2149 | rdahnke | 2022-11-29 14:50:04

Changed paths:
 M CHANGES.txt
 M cat_main1639.m
 M cat_main_APRG.m
 M cat_main_LASs.m
 M cat_main_gintnorm1639.m
 M cat_main_reportfig.m
 M cat_main_updateSPM1639.m
 M cat_surf_render2.m


Fixed:     Corrected settings to handle MP2Rage in cat_main_updateSPM1639,
           cat_main_APRG, cat_main_LASs, and cat_main_gintnorm1639.
Fixed:     Added try-catch to avoid problems in fast surface rendering.

------------------------------------------------------------------------
r2148 | rdahnke | 2022-11-27 21:31:16

Changed paths:
 M CHANGES.txt
A  batches/cat12_batch_prepana_smoothandmore.m
 M cat_conf_tools.m
 M cat_io_csv.m
A  cat_io_struct2cell.m
 M cat_stat_getCSVXMLfield.m
 M doc/cat.html
 M doc/cat.txt


Fixed:     Correct padding of cat.html.
New:       Added cat_io_struct2cell to support recursive data conversion and
           unfolding of a structure (required for XML field extraction).
Changed:   Modified cat_io_csv to support detections of field delimiter and
           handling of TSV files.
Changed:   Strong update of cat_stat_getCSVXMLfield function and the related
           matlabbatches.

------------------------------------------------------------------------
r2147 | gaser | 2022-11-24 17:13:44

Changed paths:
 M CHANGES.txt
A  cat_stat_orth_nuisance.m
 M cat_system.m


Added:   New function cat_stat_orth_nuisance.m to orthogonalize nuisance
         parameters w.r.t. covariate of interest.
Changed: Added additional trial to change file permissions of cat_system fails.
------------------------------------------------------------------------
r2146 | gaser | 2022-11-23 12:10:44

Changed paths:
 M .gitattributes
 M CHANGES.txt
A  cat_amap.mexmaca64
 M cat_conf_tools.m
A  cat_ornlm.mexmaca64
 M cat_plot_scatter.m
A  cat_sanlm.mexmaca64
 M cat_stat_spm2x.m
A  cat_vbdist.mexmaca64
A  cat_vol_downcut.mexmaca64
A  cat_vol_eidist.mexmaca64
A  cat_vol_genus0.mexmaca64
A  cat_vol_gradient3.mexmaca64
A  cat_vol_interp3f.mexmaca64
A  cat_vol_laplace3.mexmaca64
A  cat_vol_laplace3R.mexmaca64
A  cat_vol_localstat.mexmaca64
A  cat_vol_median3.mexmaca64
A  cat_vol_median3c.mexmaca64
A  cat_vol_pbtp.mexmaca64
A  cat_vol_pbtp2.mexmaca64
A  cat_vol_simgrow.mexmaca64
 M compile.m
A  templates_MNI152NLin2009cAsym/brainmask_GM.nii
A  templates_MNI152NLin2009cAsym/brainmask_GMtight.nii
 M templates_MNI152NLin2009cAsym/templates.man


Added:   Created new GM brainmask for VBM analysis in
         templates_MNI152NLin2009cAsym.
Changed: Compiled mex-files for MACA64 and updated compile.m.
Changed: Updated help text for conversion to standard normal distribution
         (z-value).
------------------------------------------------------------------------
r2145 | gaser | 2022-11-22 07:48:43

Changed paths:
 M CHANGES.txt
A  templates_MNI152NLin2009cSym/Template_0_GS.nii
A  templates_MNI152NLin2009cSym/Template_1_GS.nii
A  templates_MNI152NLin2009cSym/Template_2_GS.nii
A  templates_MNI152NLin2009cSym/Template_3_GS.nii
A  templates_MNI152NLin2009cSym/Template_4_GS.nii


Changed: Again added new symmetrical templates.

------------------------------------------------------------------------
r2144 | gaser | 2022-11-22 07:45:35

Changed paths:
 M CHANGES.txt


Changed: Again added new symmetrical templates.

------------------------------------------------------------------------
r2143 | gaser | 2022-11-22 07:35:43

Changed paths:
 M CHANGES.txt
 M Contents.m
 M doc/cat.html
 M doc/index.html


Changed: Changed server name to www.neuro.uni-jena.de in html doc.
------------------------------------------------------------------------
r2141 | gaser | 2022-11-21 23:35:20

Changed paths:
 M CHANGES.txt


Added:   Added new template folder for symmetrical MNI152NLin2009c shooting
         template for lateralization analysis.
Changed: Updated .gitattribute and .gitignore to consider new template folder
Changed: Slightly updated help text in cat_conf_tools.m.
Changed: Updated filter selection in cat_stat_diff.m to prevent trouble for 4D
         images.
Changed: Replaced error message in cat_update by simple printout.
Changed: Removed revision info from standalone zip-files in Makefile.
Fixed:   Corrected wrong coding for rotate3d in cat_surf_results.m
Fixed:   Handling of 4D data in cat_vol_ctype.m was not yet working.
------------------------------------------------------------------------
r2140 | gaser | 2022-11-21 23:06:12

Changed paths:
 M .gitattributes
 M .gitignore
 M CHANGES.txt
 M Makefile
 M cat_conf_tools.m
 M cat_stat_diff.m
 M cat_surf_results.m
 M cat_update.m
A  templates_MNI152NLin2009cSym/Template_0_GS.nii
A  templates_MNI152NLin2009cSym/Template_1_GS.nii
A  templates_MNI152NLin2009cSym/Template_2_GS.nii
A  templates_MNI152NLin2009cSym/Template_3_GS.nii
A  templates_MNI152NLin2009cSym/Template_4_GS.nii


Added:   Added new template folder for symmetrical MNI152NLin2009c shooting
         template for lateralization analysis.
Changed: Updated .gitattribute and .gitignore to consider new template folder
Changed: Slightly updated help text in cat_conf_tools.m.
Changed: Updated filter selection in cat_stat_diff.m to prevent trouble for 4D
         images.
Changed: Replaced error message in cat_update by simple printout.
Changed: Removed revision info from standalone zip-files in Makefile.
Fixed:   Corrected wrong coding for rotate3d in cat_surf_results.m
Fixed:   Handling of 4D data in cat_vol_ctype.m was not yet working.
------------------------------------------------------------------------
r2139 | rdahnke | 2022-11-18 16:02:13

Changed paths:
 M CHANGES.txt
 M cat_batch_spm.m
 M cat_batch_spm.sh
 M cat_conf_stools.m
 M cat_conf_tools.m
 M cat_io_csv.m
 M cat_io_data2mat.m
 M cat_main.m
 M cat_main_APRG.m
 M cat_main_LASs.m
 M cat_main_gintnorm1639.m
 M cat_main_updateSPM1639.m
 M cat_stat_getCSVXMLfield.m
 M cat_surf_createCS.m
AD internal/cat_defaults_fastlong.m


(1) Fixed:  Updated settings of resample/smooth batch to filter multiple input
            dependencies in cat_conf_stools.
(2) Fixed:  Extended cat_io_csv to support TSV files. Unfinished corrections in
            cat_conf_tools and cat_stat_getCSVXMLfield to improve usability for
            CSV and TSV files in general.
(3) Fixed:  Small changes and corrections in cat_io_data2mat and its dependency
            definitions but there is some bug in using dependencies as input,
            e.g., from the SPM file selector.
(4) Fixed:  Tiny corrections in cat_main and cat_main_LASs for 7T data.
(5) Fixed:  Corrected brain extraction problems of missing CSF in MP2Rage data
            in cat_main_APRG, gintnorm1639, and cat_main_updateSPM1639
(6) Fixed:  Corrected path bug in cat_surf_createCS by using the V0 rather than
            the V similar to cat_surf_createCS2).
(7) New:    Added option to cat_batch_spm.sh and cat_batch_spm.m to create
            variables before calling the matlabbatch, e.g., to use variable
            input files or parameters. Added another option to extend the matlab
            path and automatically added the path of the called batch file.
            Small bug fixes to set up parameters and catch errors.
(8) New:    Added code in cat_main_updateSPM1639 to characterize the SPM
            segmentation and store the result in the res structure that is
            saved in the CAT XML.
(9) New:    Added a batch for smoothing and downsampling of volumes and
            estimation of surface measures and resampling and smoothing.
------------------------------------------------------------------------
r2138 | gaser | 2022-11-16 23:59:37

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat12.m
 M cat_conf_tools.m
 M cat_stat_homogeneity.m
 M cat_stat_spm2x.m
 M cat_surf_coregvol2surf.m
 M doc/cat.html


Changed: Added again transformation to effect size d to cat_stat_spm2x.m, but
         extended help text and added recommendations for use.
Fixed:   Slice display in cat_stat_homogeneity.m used the wrong file order.
Fixed:   Corrected typo in cat12.m
Fixed:   Updated cat_surf_coregvol2surf.m batch with correct fieldnames.
------------------------------------------------------------------------
r2137 | gaser | 2022-11-15 00:52:39

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_stat_homogeneity.m
 M doc/cat.html
 M doc/css/main.css
 M doc/index.html


Changed: Added Quality check to the html manual and updated information about
         smoothing and matched filter theorem.
Fixed:   Corrected error in cat_stat_homogeneity.m due to wrong datacursormode
         command.
------------------------------------------------------------------------
r2136 | gaser | 2022-11-10 09:46:49

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_main_reportfig.m
 M cat_run_job1639.m
 M cat_surf_createCS2.m
 M cat_surf_fun.m
 M doc/cat.html


Fixed: Corrected typo in cat_main_reportfig.m.
Fixed: Added check whether useprior field exists.
Fixed: Added check whether fie exists to loadSurf function in
       cat_surf_createCS2.m.
Fixed: Force conversion to double type in cat_surf_fun.m.
------------------------------------------------------------------------
r2135 | gaser | 2022-11-08 23:00:18

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m
 M cat_parallelize.m
 M cat_run.m
 M cat_stat_check_cov_old.m
 M cat_stat_homogeneity.m
 M cat_surf_results.m
 M cat_surf_surf2roi.m
 M cat_vol_slice_overlay.m
 M cat_vol_slice_overlay_rgb_ui.m
 M cat_vol_slice_overlay_ui.m
R  html/icons/file_cat_log.png -> doc/icons/file_cat_log.png
R  html/icons/file_cat_report.png -> doc/icons/file_cat_report.png
R  html/icons/file_cat_report_surf.png -> doc/icons/file_cat_report_surf.png
R  html/icons/file_cat_reportlong.png -> doc/icons/file_cat_reportlong.png
R  html/icons/file_cat_xml.png -> doc/icons/file_cat_xml.png
R  html/icons/file_delete.png -> doc/icons/file_delete.png
R  html/icons/file_delete_restore.png -> doc/icons/file_delete_restore.png
R  html/icons/file_export.png -> doc/icons/file_export.png
R  html/icons/file_new.png -> doc/icons/file_new.png
R  html/icons/file_open.png -> doc/icons/file_open.png
R  html/icons/file_pdf.png -> doc/icons/file_pdf.png
R  html/icons/file_print.png -> doc/icons/file_print.png
R  html/icons/file_save.png -> doc/icons/file_save.png
R  html/icons/file_search.png -> doc/icons/file_search.png
R  html/icons/file_spm_view.png -> doc/icons/file_spm_view.png
R  html/icons/file_spm_view_p0.png -> doc/icons/file_spm_view_p0.png
R  html/icons/file_surf.png -> doc/icons/file_surf.png
R  html/icons/file_surfc.png -> doc/icons/file_surfc.png
R  html/icons/greenarrowicon.png -> doc/icons/greenarrowicon.png
R  html/icons/list_del.png -> doc/icons/list_del.png
R  html/icons/list_new.png -> doc/icons/list_new.png
R  html/icons/redo.png -> doc/icons/redo.png
R  html/icons/refresh.png -> doc/icons/refresh.png
R  html/icons/settings.png -> doc/icons/settings.png
R  html/icons/status_failed.old.png -> doc/icons/status_failed.old.png
R  html/icons/status_failed.png -> doc/icons/status_failed.png
R  html/icons/status_forbiden.png -> doc/icons/status_forbiden.png
R  html/icons/status_help.png -> doc/icons/status_help.png
R  html/icons/status_help2.png -> doc/icons/status_help2.png
R  html/icons/status_info.png -> doc/icons/status_info.png
R  html/icons/status_passed.png -> doc/icons/status_passed.png
R  html/icons/status_warning_hard.png -> doc/icons/status_warning_hard.png
R  html/icons/status_warning_soft.png -> doc/icons/status_warning_soft.png
R  html/icons/tool_data_cursor.png -> doc/icons/tool_data_cursor.png
R  html/icons/tool_fit.png -> doc/icons/tool_fit.png
R  html/icons/tool_hand.png -> doc/icons/tool_hand.png
R  html/icons/tool_pointer.png -> doc/icons/tool_pointer.png
R  html/icons/tool_zoom_in.png -> doc/icons/tool_zoom_in.png
R  html/icons/tool_zoom_out.png -> doc/icons/tool_zoom_out.png
R  html/icons/trash_auto.png -> doc/icons/trash_auto.png
R  html/icons/trash_col_add.png -> doc/icons/trash_col_add.png
R  html/icons/trash_col_rm.png -> doc/icons/trash_col_rm.png
R  html/icons/trash_row_add.png -> doc/icons/trash_row_add.png
R  html/icons/trash_row_rm.png -> doc/icons/trash_row_rm.png
R  html/icons/trash_tip_add.png -> doc/icons/trash_tip_add.png
R  html/icons/trash_tip_rm.png -> doc/icons/trash_tip_rm.png
R  html/icons/undo.png -> doc/icons/undo.png


Changed: Moved icons folder from html to doc.
Changed: Create logs folder in current directory rather than in cat12.
Changed: Changed path of T1 image in cat_vol_slice_overlay_ui.m
Changed: Use cat_progress_bar in cat_surf_surf2roi.m.
Fixed:   Corrected outofrange field in cat_vol_slice_overlay.m.
Fixed:   Added try/catch to disable interpreter in cat_surf_results.m because
         it's not working on all Matlab versions.
Fixed:   Commented out multi-subject imcalc in cat_conf_tools.m because it was
         not working with newer SPM12 versions.
------------------------------------------------------------------------
r2133 | gaser | 2022-11-08 00:47:58

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_update.m
 M doc/cat.html


Changed: Some small changes to cat_update.m.
------------------------------------------------------------------------
r2131 | gaser | 2022-11-08 00:16:30

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat_update.m
 M doc/cat.html
 M spm_cat12.m


Changed: Added old html folder and PDF manual to file that are removed during
         update.
------------------------------------------------------------------------
r2130 | gaser | 2022-11-08 00:03:30

Changed paths:
 M CHANGES.txt
 M doc/cat.html


Changed: Updated version number.
------------------------------------------------------------------------
r2129 | gaser | 2022-11-08 00:02:32

Changed paths:
 M CHANGES.txt
 M Makefile
 M doc/index.html


Changed: Updated CAT12 HTML doc.
Changed: Updated version number.
------------------------------------------------------------------------
r2128 | gaser | 2022-11-07 22:48:43

Changed paths:
 M CHANGES.txt
A  doc/css/cat.css


Added: Added css style file for entry page.
------------------------------------------------------------------------
r2127 | gaser | 2022-11-07 22:48:21

Changed paths:
 M CHANGES.txt
 M doc/cat.html


Added: Added css style file for entry page.
------------------------------------------------------------------------
r2126 | gaser | 2022-11-07 22:44:23

Changed paths:
 M CHANGES.txt
 M Contents.m
 M Makefile
 M cat12.m
 M cat_install_tfce.m
 M cat_update.m
 M doc/cat.html
AM doc/cat.txt
 M doc/css/main.css
 M doc/index.html
 M spm_cat12.m


Changed: Many changes to implement the new html help.
Changed: Updated Makefile to consider new html help.
Changed: Updated and moved cat.txt from html to doc folder.
Added:   Added css style file for entry page.
------------------------------------------------------------------------
r2125 | gaser | 2022-10-26 13:45:37

Changed paths:
 M CHANGES.txt
 M cat_batch_bids.sh
 M cat_plot_histogram.m


Changed: Included some of Jussi Tohkas modifications into cat_batch_bids.sh.
Fixed:   Reading of Freesurfer and gifti data in cat_plot_histogram was
         erroneous.
------------------------------------------------------------------------
r2124 | gaser | 2022-10-24 11:52:19

Changed paths:
 M CHANGES.txt
 M Makefile
 M cat_conf_tools.m
 M cat_progress_bar.m
 M cat_stat_homogeneity.m
 M doc/index.html
 M update_revision.sh


Changed: Renamed the multiple tools to check homogeneity.
Changed: Added description of output to cat_stat_homogeneity.m.
Changed: Updated html doc.
Fixed:   Added try command to waitbar-call in cat_progress_bar to prevent errors
         if progress window was closed.


------------------------------------------------------------------------
r2123 | rdahnke | 2022-10-20 10:53:46

Changed paths:
 M CHANGES.txt
 M cat_batch_long.m
 M cat_batch_long.sh
 M cat_conf_long.m


Fixed:  Corrected handling of printlong variable in long shell batch.
------------------------------------------------------------------------
r2122 | gaser | 2022-10-18 17:26:11

Changed paths:
 M CHANGES.txt
 M doc/css/main.css
 M doc/index.html


Changed: Updated CAT12 HTML documentation.

------------------------------------------------------------------------
r2121 | gaser | 2022-10-18 15:34:39

Changed paths:
 M CHANGES.txt
 M Makefile
 M doc/index.html


Changed: Updated CAT12 HTML documentation.

------------------------------------------------------------------------
r2120 | gaser | 2022-10-18 12:44:04

Changed paths:
 M CHANGES.txt
 M doc/index.html


Changed: Updated CAT12 HTML documentation.

------------------------------------------------------------------------
r2118 | gaser | 2022-10-18 11:04:54

Changed paths:
 M .gitattributes
 M CHANGES.txt
 M cat_conf_ROI.m
 M cat_conf_stools.m
 M cat_defaults.m
 M cat_surf_results.m
 M doc/css/main.css
 M doc/index.html
 M templates_MNI152NLin2009cAsym/thalamic_nuclei.nii


Changed: Added support for RGB overlay to cat_surf_results.m using 'rgb' option.
Changed: Moved option for surface resample size to expert mode.
Changed: Updated information about new thalamic nuclei atlas.
Changed: Updated CAT12 HTML documentation.

------------------------------------------------------------------------
r2117 | rdahnke | 2022-10-17 17:05:15

Changed paths:
 M CHANGES.txt
 M cat_io_cmd.m


Fixed:  Corrected output style setting in cat_io_cmd.
------------------------------------------------------------------------
r2116 | gaser | 2022-10-17 14:25:56

Changed paths:
 M CHANGES.txt
 M cat_conf_ROI.m
 M cat_defaults.m
A  doc/cat.html
A  doc/css/fontawesome-all.min.css
A  doc/css/main.css
A  doc/disclaimer.html
A  doc/images/CAT.png
A  doc/images/CAT_Error_Report.jpg
A  doc/images/CAT_PBT_for_SPM.png
A  doc/images/CAT_Report.jpg
A  doc/images/CAT_surf_atlas_DKT40.png
A  doc/images/CAT_surf_atlas_Desikan-Killiany.png
A  doc/images/CAT_surf_atlas_Destrieux.png
A  doc/images/CAT_surf_atlas_PALS-B12-Brodmann.png
A  doc/images/CAT_surf_atlas_PALS-B12-Lobes.png
A  doc/images/CAT_surf_atlas_aal.png
A  doc/images/CAT_surf_atlas_hammers.png
A  doc/images/CAT_surf_atlas_lpba40.png
A  doc/images/CAT_surf_atlas_mori.png
A  doc/images/CAT_surf_atlas_neuromorphometrics.png
A  doc/images/Gyral_blurring.png
A  doc/images/Problems_in_7_Tesla.png
A  doc/images/Sulcal_blurring.png
A  doc/images/analyse_methods.png
A  doc/images/background_biasreal.png
A  doc/images/background_morphops.png
A  doc/images/background_noise.png
A  doc/images/batch_gui.jpg
A  doc/images/cat_SLC_msk_c0009s0010t01A.png
A  doc/images/cat_bg.jpg
A  doc/images/cat_extract_addition_surface_parameter.png
A  doc/images/cat_gui.png
A  doc/images/cat_hd02.png
A  doc/images/cat_hd02blue.png
A  doc/images/cat_hd02blue2.png
A  doc/images/cat_hd02cyan.png
A  doc/images/cat_hd02green.png
A  doc/images/cat_hd02orange.png
A  doc/images/cat_hd02purple.png
A  doc/images/cat_hd02red.png
A  doc/images/cat_hd02yellow.png
A  doc/images/cat_logo.png
A  doc/images/cat_long_pipeline.png
A  doc/images/cat_long_pipelines.png
A  doc/images/cat_long_report_plasticity-aging_ADNI011S0003.jpg
A  doc/images/cat_long_report_scannerdifferences_ADNI002S0559.jpg
A  doc/images/cat_methods_catsimple.png
A  doc/images/cat_methods_downsampling.jpg
A  doc/images/cat_methods_postmortem.jpg
A  doc/images/cat_processing_pipeline.png
A  doc/images/cat_processing_steps.png
A  doc/images/cat_qa_expert.png
A  doc/images/cat_qa_rating-distribution.png
A  doc/images/cat_qa_rating-table.jpg
A  doc/images/cat_stat_checkcov_00_overview.png
A  doc/images/cat_stat_checkcov_01_batch.png
A  doc/images/cat_stat_checkcov_02_command.png
A  doc/images/cat_stat_checkcov_03_checkcov.png
A  doc/images/cat_stat_checkcov_04_boxplot01_MNC.png
A  doc/images/cat_stat_checkcov_04_boxplot02_IQR.png
A  doc/images/cat_stat_checkcov_05_check_01_original.png
A  doc/images/cat_stat_checkcov_07_exclusion.png
A  doc/images/cat_surf_vx2surf_evalGM.png
A  doc/images/cat_surf_vx2surf_smoothing.png
A  doc/images/cat_surf_vx2surf_vol-int-dist.png
A  doc/images/cat_tst_reg_boxplot.png
A  doc/images/cat_tst_seg_BWP_boxplot.png
A  doc/images/cat_tst_seg_BWP_detail.png
A  doc/images/cat_tst_seg_bwp_ana.png
A  doc/images/cat_tst_seg_bwp_boxplot_para.png
A  doc/images/cat_tst_seg_bwp_boxplot_para_CAT.png
A  doc/images/cat_tst_seg_bwp_boxplot_para_SPM.png
A  doc/images/cat_tst_seg_bwp_detail_para.png
A  doc/images/cat_tst_seg_exp_boxplot.png
A  doc/images/cat_tst_seg_exp_boxplot_para_CAT.png
A  doc/images/cat_tst_seg_exp_boxplot_para_SPM.png
A  doc/images/cat_tst_seg_exp_boxplot_para_WMH.png
A  doc/images/cat_tst_seg_exp_detail.png
A  doc/images/cat_tst_seg_exp_detail_para.png
A  doc/images/cat_tst_seg_ibsr_boxplot.png
A  doc/images/cat_tst_seg_ibsr_detail.png
A  doc/images/cat_tst_seg_sve_boxplot.png
A  doc/images/cat_tst_seg_sve_detail.png
A  doc/images/cat_vol_correct_slice_scaling_768.png
A  doc/images/catlongreportj_mwp1r.jpg
A  doc/images/catreport_Collins.jpg
A  doc/images/catreportj_OAS1_0031_MR1_mpr_n4_anon_sbj_111_WMHC0.jpg
A  doc/images/catreportj_OAS1_0031_MR1_mpr_n4_anon_sbj_111_WMHC1.jpg
A  doc/images/catreportj_OAS1_0031_MR1_mpr_n4_anon_sbj_111_WMHC2.jpg
A  doc/images/catreportj_OAS1_0031_MR1_mpr_n4_anon_sbj_111_WMHC3.jpg
A  doc/images/contact.jpg
A  doc/images/contact_small.jpg
A  doc/images/cortical_measures.png
A  doc/images/gyrification_index.png
A  doc/images/home.jpg
A  doc/images/human_brain.png
A  doc/images/images.jpg
A  doc/images/model_2sample.png
A  doc/images/model_anova2x2.png
A  doc/images/model_interact.png
A  doc/images/model_interact_poly.png
A  doc/images/model_long1.png
A  doc/images/model_long2.png
A  doc/images/model_long_cov.png
A  doc/images/model_mult_reg.png
A  doc/images/model_mult_reg2.png
A  doc/images/neonates.png
A  doc/images/non_orthogonal.png
A  doc/images/ortho.png
A  doc/images/people.jpg
A  doc/images/preprocessing.png
A  doc/images/research.jpg
A  doc/images/spm_gui.png
A  doc/images/vbm.jpg
A  doc/index.html
A  doc/js/breakpoints.min.js
A  doc/js/browser.min.js
A  doc/js/jquery.min.js
A  doc/js/main.js
A  doc/js/util.js
A  doc/webfonts/fa-brands-400.eot
A  doc/webfonts/fa-brands-400.svg
A  doc/webfonts/fa-brands-400.ttf
A  doc/webfonts/fa-brands-400.woff
A  doc/webfonts/fa-brands-400.woff2
A  doc/webfonts/fa-regular-400.eot
A  doc/webfonts/fa-regular-400.svg
A  doc/webfonts/fa-regular-400.ttf
A  doc/webfonts/fa-regular-400.woff
A  doc/webfonts/fa-regular-400.woff2
A  doc/webfonts/fa-solid-900.eot
A  doc/webfonts/fa-solid-900.svg
A  doc/webfonts/fa-solid-900.ttf
A  doc/webfonts/fa-solid-900.woff
A  doc/webfonts/fa-solid-900.woff2
A  templates_MNI152NLin2009cAsym/thalamic_nuclei.csv
A  templates_MNI152NLin2009cAsym/thalamic_nuclei.nii
A  templates_MNI152NLin2009cAsym/thalamic_nuclei.txt
 M templates_MNI152NLin2009cAsym/thalamus.txt


Added: Added new atlas for thalamic nuclei using hi-res T2.
Added: Added new html documentation.

------------------------------------------------------------------------
r2115 | gaser | 2022-10-14 17:12:37

Changed paths:
 M CHANGES.txt
 M cat_conf_extopts.m


Changed: Moved some rarely used CAT12 options to expert mode.
------------------------------------------------------------------------
r2114 | gaser | 2022-10-14 15:50:10

Changed paths:
 M CHANGES.txt
R  templates_volumes/Schaefer2018_100Parcels_17Networks_order.csv -> templates_volumes_old/Schaefer2018_100Parcels_17Networks_order.csv
R  templates_volumes/Schaefer2018_100Parcels_17Networks_order.nii -> templates_volumes_old/Schaefer2018_100Parcels_17Networks_order.nii
R  templates_volumes/Schaefer2018_200Parcels_17Networks_order.csv -> templates_volumes_old/Schaefer2018_200Parcels_17Networks_order.csv
R  templates_volumes/Schaefer2018_200Parcels_17Networks_order.nii -> templates_volumes_old/Schaefer2018_200Parcels_17Networks_order.nii
R  templates_volumes/Schaefer2018_400Parcels_17Networks_order.csv -> templates_volumes_old/Schaefer2018_400Parcels_17Networks_order.csv
R  templates_volumes/Schaefer2018_400Parcels_17Networks_order.nii -> templates_volumes_old/Schaefer2018_400Parcels_17Networks_order.nii
R  templates_volumes/Schaefer2018_600Parcels_17Networks_order.csv -> templates_volumes_old/Schaefer2018_600Parcels_17Networks_order.csv
R  templates_volumes/Schaefer2018_600Parcels_17Networks_order.nii -> templates_volumes_old/Schaefer2018_600Parcels_17Networks_order.nii
R  templates_volumes/TPM_Age11.5.nii -> templates_volumes_old/TPM_Age11.5.nii
R  templates_volumes/Template_0_IXI555_MNI152_GS.nii -> templates_volumes_old/Template_0_IXI555_MNI152_GS.nii
R  templates_volumes/Template_1_IXI555_MNI152.nii -> templates_volumes_old/Template_1_IXI555_MNI152.nii
R  templates_volumes/Template_1_IXI555_MNI152_GS.nii -> templates_volumes_old/Template_1_IXI555_MNI152_GS.nii
R  templates_volumes/Template_2_IXI555_MNI152.nii -> templates_volumes_old/Template_2_IXI555_MNI152.nii
R  templates_volumes/Template_2_IXI555_MNI152_GS.nii -> templates_volumes_old/Template_2_IXI555_MNI152_GS.nii
R  templates_volumes/Template_3_IXI555_MNI152.nii -> templates_volumes_old/Template_3_IXI555_MNI152.nii
R  templates_volumes/Template_3_IXI555_MNI152_GS.nii -> templates_volumes_old/Template_3_IXI555_MNI152_GS.nii
R  templates_volumes/Template_4_IXI555_MNI152.nii -> templates_volumes_old/Template_4_IXI555_MNI152.nii
R  templates_volumes/Template_4_IXI555_MNI152_GS.nii -> templates_volumes_old/Template_4_IXI555_MNI152_GS.nii
R  templates_volumes/Template_5_IXI555_MNI152.nii -> templates_volumes_old/Template_5_IXI555_MNI152.nii
R  templates_volumes/Template_6_IXI555_MNI152.nii -> templates_volumes_old/Template_6_IXI555_MNI152.nii
R  templates_volumes/Template_T1_IXI555_MNI152_GS.nii -> templates_volumes_old/Template_T1_IXI555_MNI152_GS.nii
R  templates_volumes/aal3.csv -> templates_volumes_old/aal3.csv
R  templates_volumes/aal3.nii -> templates_volumes_old/aal3.nii
R  templates_volumes/aal3.txt -> templates_volumes_old/aal3.txt
R  templates_volumes/anatomy3.csv -> templates_volumes_old/anatomy3.csv
R  templates_volumes/anatomy3.nii -> templates_volumes_old/anatomy3.nii
R  templates_volumes/anatomy3.txt -> templates_volumes_old/anatomy3.txt
R  templates_volumes/brainmask.nii -> templates_volumes_old/brainmask.nii
R  templates_volumes/cat.nii -> templates_volumes_old/cat.nii
R  templates_volumes/cat_strokelesions_ATLAS303.nii -> templates_volumes_old/cat_strokelesions_ATLAS303.nii
R  templates_volumes/cat_wmh.nii -> templates_volumes_old/cat_wmh.nii
R  templates_volumes/cat_wmh_miccai2017.nii -> templates_volumes_old/cat_wmh_miccai2017.nii
R  templates_volumes/cobra.csv -> templates_volumes_old/cobra.csv
R  templates_volumes/cobra.nii -> templates_volumes_old/cobra.nii
R  templates_volumes/cobra.txt -> templates_volumes_old/cobra.txt
R  templates_volumes/hammers.csv -> templates_volumes_old/hammers.csv
R  templates_volumes/hammers.nii -> templates_volumes_old/hammers.nii
R  templates_volumes/hammers.txt -> templates_volumes_old/hammers.txt
R  templates_volumes/ibsr.csv -> templates_volumes_old/ibsr.csv
R  templates_volumes/ibsr.nii -> templates_volumes_old/ibsr.nii
R  templates_volumes/ibsr.txt -> templates_volumes_old/ibsr.txt
R  templates_volumes/julichbrain.csv -> templates_volumes_old/julichbrain.csv
R  templates_volumes/julichbrain.nii -> templates_volumes_old/julichbrain.nii
R  templates_volumes/julichbrain.txt -> templates_volumes_old/julichbrain.txt
R  templates_volumes/lpba40.csv -> templates_volumes_old/lpba40.csv
R  templates_volumes/lpba40.nii -> templates_volumes_old/lpba40.nii
R  templates_volumes/lpba40.txt -> templates_volumes_old/lpba40.txt
R  templates_volumes/mori.csv -> templates_volumes_old/mori.csv
R  templates_volumes/mori.nii -> templates_volumes_old/mori.nii
R  templates_volumes/mori.txt -> templates_volumes_old/mori.txt
R  templates_volumes/neuromorphometrics.csv -> templates_volumes_old/neuromorphometrics.csv
R  templates_volumes/neuromorphometrics.nii -> templates_volumes_old/neuromorphometrics.nii
R  templates_volumes/neuromorphometrics.txt -> templates_volumes_old/neuromorphometrics.txt
R  templates_volumes/schaefer.txt -> templates_volumes_old/schaefer.txt
R  templates_volumes/templates.man -> templates_volumes_old/templates.man


Changed: Renamed templates_volumes to templates_volumes-old because it#s not
         used anymore.
------------------------------------------------------------------------
r2113 | gaser | 2022-10-10 11:47:33

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat12.m
 M cat_long_main.m
 M cat_long_multi_run.m
 M html/cat.html


Fixed: Corrected typos in cat_long_main.m and cat_long_multi_run.m.
------------------------------------------------------------------------
r2109 | gaser | 2022-10-05 00:47:51

Changed paths:
 M CHANGES.txt
 M Contents.m
 M cat12.m
 M cat_spm_results_ui.m
 M html/cat.html


Changed: Updated remaining hardcoded toolbox paths for TFCE.
------------------------------------------------------------------------
r2108 | gaser | 2022-10-05 00:29:40

Changed paths:
 M CHANGES.txt
 M cat12.m
 M cat_surf_render.m
 M cat_surf_render2.m
 M cat_update.m
 M cat_version.m
 M spm_cat12.m


Changed: Updated remaining hardcoded toolbox paths for CAT12.
------------------------------------------------------------------------
r2107 | gaser | 2022-10-05 00:12:40

Changed paths:
 M CHANGES.txt
 M cat12.m
 M cat_conf_stools.m
 M cat_conf_stoolsexp.m
 M cat_defaults.m
 M cat_io_FreeSurfer.m
 M cat_io_checkdepfiles.m
 M cat_io_xml.m
 M cat_long_main.m
 M cat_long_multi_run.m
 M cat_parallelize.m
 M cat_plot_histogram.m
 M cat_roi_roi2surf.m
 M cat_roi_values2surf.m
 M cat_run.m
 M cat_simple.m
 M cat_spm_results_ui.m
 M cat_stat_analyze_ROIs.m
 M cat_stat_check_cov_old.m
 M cat_stat_cva_ui.m
 M cat_stat_homogeneity.m
 M cat_stat_spm.m
 M cat_stat_spm2x.m
 M cat_surf_avg.m
 M cat_surf_calc.m
 M cat_surf_createCS.m
 M cat_surf_createCS2.m
 M cat_surf_create_TPM_hull_surface.m
 M cat_surf_display.m
 M cat_surf_flipsides.m
 M cat_surf_fun.m
 M cat_surf_gyrification.m
 M cat_surf_info.m
 M cat_surf_map_atlas.m
 M cat_surf_parameters.m
 M cat_surf_render.m
 M cat_surf_render2.m
 M cat_surf_resamp.m
 M cat_surf_resamp_freesurfer.m
 M cat_surf_results.m
 M cat_surf_smooth.m
 M cat_surf_surf2roi.m
 M cat_surf_vol2surf.m
 M cat_system.m
 M cat_tst_cattest.m
 M cat_vol_slice_overlay_ui.m
 M spm_cat12.m
 M standalone/cat_standalone_segment_long.m
 M standalone/cat_standalone_simple.m


Changed: Updated hardcoded toolbox path for CAT12.
------------------------------------------------------------------------
r2106 | rdahnke | 2022-10-04 16:27:55

Changed paths:
 M CHANGES.txt
 M cat_conf_long.m
 M cat_conf_tools.m
 M cat_long_main.m
 M cat_long_multi_run.m
 M cat_long_report.m


New:   Added an option in the longitudinal processing (cat_conf_long) and the
       longitudinal report batch (cat_conf_tools) to print a longitudinal
       report using default print setting of the cross-sectional report.
       Although the changes in cat_long_report looks huge it is only an
       additional if-block.
------------------------------------------------------------------------
r2105 | gaser | 2022-09-29 15:17:42

Changed paths:
 M CHANGES.txt
 M Contents.m
A  cat_batch_bids.sh
 M cat_batch_cat.sh
 M cat_batch_long.sh
 M cat_batch_spm.sh
 M cat_conf_factorial.m
 M cat_stat_homogeneity.m
 M check_pipeline.sh
 M distribute_to_server.sh
 M html/cat.html
 M spm_cat12.m


Added:   Added new shell script to process BIDS data.
Changed: Updated help for shell scripts.
Fixed:   Corrected check for voxel-wise covariates in cat_conf_factorial.m
Fixed:   Corrected some smaller issues in cat_stat_homogeneity.m
------------------------------------------------------------------------
r2104 | gaser | 2022-08-30 16:24:26

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m
 M cat_plot_boxplot.m
 M cat_plot_scatter.m
 M cat_stat_spm2x.m
 M cat_surf_results.m
 M cat_vol_slice_overlay.m


Changed: Removed SPM12 neuromorphometrics atlas from lists to avoid confusion.
Changed: Added display of p-values in cat_vol_slice_overlay.m and
         cat_stat_spm2x.m if available.
Changed: Added check for updating slices whether values exceed threshold.
Changed: Updated use of color in cat_plot_scatter.m.
Changed: Disable KDE estimation for less than 5 data points.
------------------------------------------------------------------------
r2103 | gaser | 2022-08-28 11:11:25

Changed paths:
 M CHANGES.txt
 M cat_conf_factorial.m
 M cat_plot_scatter.m


Changed: Updated help text for cat_conf_factorial.m.
Changed: Slightly changed lower xlim in cat_plot_scatter to give more space if
         data min is 0.
------------------------------------------------------------------------
r2102 | gaser | 2022-08-25 23:34:52

Changed paths:
 M CHANGES.txt
 M cat_plot_scatter.m


Changed: Added new options to cat_plot_scatter.m:
          - option to distinct between different groups
          - option to define names
          - option to show legend
Changed: Removed image and contour plot from cat_plot_scatter.m.
------------------------------------------------------------------------
r2101 | gaser | 2022-08-24 15:19:35

Changed paths:
 M CHANGES.txt
 M Makefile
 M cat_surf_createCS2.m
 M cat_vol_glassbrain.m
 M cat_vol_img2mip.m
 M spm_cat12.m


Changed: Force to use PET modality in CAT12 to avoid problems of very low
         variance in spm_spm.m.
Changed: Renamed cat12-html to cat12-help.
Changed: Mimimized loading of mat-file in cat_vol_galssbrain.m.
Changed: Added check for result of CAT_SeparatePolygon in cat_surf_createCS2.m
         because sometimes CAT_SeparatePolygon fails and we have to use the
         original raw file.
Fixed:   Added cbar-flag to defaults in cat_vol_img2mip.m.
------------------------------------------------------------------------
r2100 | rdahnke | 2022-08-23 13:59:53

Changed paths:
 M CHANGES.txt
 M cat_stat_homogeneity.m


Fixed:   Extended file search to support BIDS in cat_stat_homogeneity.
         Display segmentation also if no raw images were available.
         Added colorful output, warnings and errors to improve readability.
------------------------------------------------------------------------
r2099 | gaser | 2022-08-19 16:32:54

Changed paths:
 M CHANGES.txt
 M cat_surf_render.m


Fixed: Corrected use of template if no vertices are found in cat_surf_render.m.
------------------------------------------------------------------------
r2098 | rdahnke | 2022-08-19 11:43:55

Changed paths:
 M CHANGES.txt
A  cat_vol_mimcalc.m


New:    Added cat_vol_mimcalc to use the SPM imcalc batch for multiple subjects.
------------------------------------------------------------------------
r2097 | gaser | 2022-08-19 10:54:44

Changed paths:
 M CHANGES.txt
 M cat_plot_boxplot.m
 M cat_surf_results.m


Changed: Updated line colors for connected time points in cat_plot_boxplot.m
         and added transparency if available.
Changed: Added connecting time points for long. designs in cat_surf_results.m.
------------------------------------------------------------------------
r2096 | gaser | 2022-08-19 01:09:58

Changed paths:
 M CHANGES.txt
 M cat_plot_boxplot.m
 M cat_stat_check_SPM.m
 M cat_stat_confplot_spm.m
 M cat_stat_homogeneity.m
 M cat_surf_results.m


Changed: Extended cat_plot_boxplot to use a matrix xX.I from SPM.mat to draw
         connected lines between time points of each subject and group.
Changed: Updated check for subject and group effects in matrix xX.I in
         cat_stat_check_SPM.m, cat_stat_confplot_spm.m and cat_surf_results.m.
------------------------------------------------------------------------
r2095 | gaser | 2022-08-18 16:28:35

Changed paths:
 M CHANGES.txt
 M cat_surf_results.m
 M cat_vol_slice_overlay.m


Changed: Try to set the interpreter to 'none' in cat_surf_results.m
------------------------------------------------------------------------
r2094 | gaser | 2022-08-18 15:05:37

Changed paths:
 M CHANGES.txt
 M cat_stat_homogeneity.m


Fixed:   Removed implicite mask from cat_stat_homogeneity, because it wasn't
         correctly working.
Changed: Use new figure by default in cat_stat_homogeneity.m, but allow to
         disable this.
------------------------------------------------------------------------
r2093 | gaser | 2022-08-18 11:53:37

Changed paths:
 M CHANGES.txt
 M cat_plot_boxplot.m
 M cat_plot_scatter.m


Chamged: Many changes to cat_plot_scatter.m:
           - added new options to set color and fontsize and to save plot as image
           - changed default setting for 'filled' and also changed syntax to be
             more compatible to scatter function
           - confidence interval is not plotted with transparency and some more
             space to corners
Changed: Corrected order of colors for horizontal violin plot and corrected slight
         skew of density plot.
------------------------------------------------------------------------
r2092 | gaser | 2022-08-16 23:25:04

Changed paths:
 M CHANGES.txt
 M cat_surf_results.m


Fixed: Corrected some issues with datatip and coorbar in cat_surf_results.m.
------------------------------------------------------------------------
r2091 | gaser | 2022-08-16 18:10:01

Changed paths:
 M CHANGES.txt
 M cat_plot_boxplot.m
 M cat_plot_scatter.m
 M cat_surf_results.m
 M cat_vol_slice_overlay.m


Changed: Added dark color mode to cat_plot_boxplot.m.
Changed: Updated handling of different designs in cat_surf_results.m.
------------------------------------------------------------------------
r2090 | gaser | 2022-08-16 15:37:42

Changed paths:
 M CHANGES.txt
 M cat_io_volctype.m
 M cat_io_xml.m
 M cat_plot_histogram.m
 M cat_stat_check_SPM.m
 M cat_stat_homogeneity.m
 M cat_surf_results.m
 M cat_vol_slice_overlay.m
R  cg_create_MPM.m -> internal/cg_create_MPM.m
R  cg_io_send_to_server.m -> internal/cg_io_send_to_server.m


Changed: Changed some function back to use of spm_progress_bar where calls are
         made during preprocessing.
Changed: Set cat_plot_scatter to defined figure in cat_plot_histogram to
         prevent opening of new windows.
Changed: Added mask field SPM.xM to cat_stat_check_SPM to allow masking for
         calls of cat_stat_homogeneity.m and changed scaling of design matrix.
Changed: Suppressed call to spm_input in cat_vol_slice_overlay.m if not needed.
Changed: Moved some older tools to internal.
Fixed:   Solved display issues in cat_surf_results if no results survived.

------------------------------------------------------------------------
r2089 | gaser | 2022-08-15 23:53:25

Changed paths:
 M CHANGES.txt
 M cat_long_createTPM.m
 M cat_main_clean_gwc.m
 M cat_main_clean_gwc1639.m
 M cat_main_reportcmd.m
 M cat_main_updateSPM.m
 M cat_main_updateSPM1639.m
 M cat_progress_bar.m
 M cat_run_job.m
 M cat_run_job1639.m
 M cat_run_job_APRGs.m
 M cat_spm_preproc_write8.m
 M cat_spm_shoot_template.m
 M cat_stat_homogeneity.m
 M cat_surf_results.m
 M cat_surf_surf2roi.m
 M cat_vol_headtrimming.m
 M cat_vol_imcalc.m
 M cat_vol_maskimage.m
 M cat_vol_sanlm.m
 M cat_vol_sanlm2.m


Changed: Suppress output of cat_progress_bar for values close to 0%.
Changed: Changed many cat_progress_bar calls back to spm_progress_bar because
         during preprocessing multiple calls to cat_progress_bar are annoying.
Fixed:   Corrected bug in cat_surf_results.m for drawing log-scale for even
         number of XTick values.
Fixed:   Corrected some smaller bugs in cat_stat_homogeneity.m for meshes.

------------------------------------------------------------------------
r2088 | gaser | 2022-08-15 12:25:36

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m
 M cat_stat_spm2x.m


Changed: Updated help text.
------------------------------------------------------------------------
r2087 | gaser | 2022-08-12 17:28:21

Changed paths:
 M CHANGES.txt
 M cat_stat_homogeneity.m


Changed: Added sample information to slice data field in cat_stat_homogeneity.m.
------------------------------------------------------------------------
r2086 | gaser | 2022-08-12 17:10:33

Changed paths:
 M CHANGES.txt
 M cat_io_cgw2seg.m
 M cat_io_data2mat.m
 M cat_io_img2nii.m
 M cat_io_volctype.m
 M cat_io_xml.m
 M cat_long_createTPM.m
 M cat_main_clean_gwc.m
 M cat_main_clean_gwc1639.m
 M cat_main_registration.m
 M cat_main_reportcmd.m
 M cat_main_updateSPM.m
 M cat_main_updateSPM1639.m
 M cat_parallelize.m
 M cat_plot_boxplot.m
A  cat_progress_bar.m
 M cat_roi_roi2surf.m
 M cat_run.m
 M cat_run_job.m
 M cat_run_job1639.m
 M cat_run_job_APRGs.m
 M cat_spm_preproc_write8.m
 M cat_spm_shoot_template.m
 M cat_stat_IQR.m
 M cat_stat_TIV.m
 M cat_stat_analyze_ROIs.m
 M cat_stat_check_cov_old.m
 M cat_stat_homogeneity.m
 M cat_stat_quality_measures.m
 M cat_stat_showslice_all.m
 M cat_surf_avg.m
 M cat_surf_calc.m
 M cat_surf_parameters.m
 M cat_surf_resamp.m
 M cat_surf_smooth.m
 M cat_surf_surf2roi.m
 M cat_surf_vol2surf.m
 M cat_surf_vx2surf.m
 M cat_vol_correct_slice_scaling.m
 M cat_vol_createTPM.m
R  cat_vol_glass.m -> cat_vol_glassbrain.m
 M cat_vol_headtrimming.m
 M cat_vol_imcalc.m
 M cat_vol_img2mip.m
 M cat_vol_maskimage.m
 M cat_vol_reduceRes.m
 M cat_vol_sanlm.m
 M cat_vol_sanlm2.m
 M cg_create_MPM.m


Added:   New function cat_progress_bar.m to replace spm_progress_bar.m.
Changed: Replaced all spm_progress_bar calls by cat_progress_bar.
Changed: Renamed cat_vol_glass.m to cat_vol_glassbrain.m.
Changed: Updated help text for cat_plot_boxplot.m.
Changed: Many changes to cat_stat_homogeneity.m
           - use preloading of slice data to speed up data selection
           - moved and changed ui-elements
           - added more display of more parameters to slice data field
------------------------------------------------------------------------
r2085 | rdahnke | 2022-08-12 13:08:57

Changed paths:
 M CHANGES.txt
 M cat_stat_homogeneity.m


Changed:    Some visual suggestions in cat_stat_homoeneity and a small bug fix.
------------------------------------------------------------------------
r2084 | gaser | 2022-08-11 17:28:09

Changed paths:
 M CHANGES.txt
 M cat_stat_homogeneity.m


Fixed:  Corrected scaling issues of QM-scores in cat_stat_homogeneity.m.
------------------------------------------------------------------------
r2083 | gaser | 2022-08-11 17:14:46

Changed paths:
 M CHANGES.txt
 M cat_surf_results.m


Fixed:  Corrected selection of slice rows/columns after automatically estimation
        of local maxima in cat_surf_results.m.
------------------------------------------------------------------------
r2082 | gaser | 2022-08-11 16:03:51

Changed paths:
 M CHANGES.txt
 M Makefile
 M cat_surf_results.m
AM cat_vol_glass.m
 M cat_vol_img2mip.m
 M cat_vol_slice_overlay.m
A  glass_brain.mat


Added:   Added new function cat_vol_glass.m to visualize glassbrain using a
         modified version of spm_glass.
Changed: Modified cat_vol_img2mip.m to support cat_vol_glass.m.
Changed: Added OV to output argument in cat_vol_slice_overlay.m to allow
         to update OV fields such as OV.slices_str.
Changed: Some changes to cat_surf_results.m to consider new functionality.
------------------------------------------------------------------------
r2081 | gaser | 2022-08-11 12:11:50

Changed paths:
 M CHANGES.txt
 M cat12.m
 M cat_surf_results.m
 M cat_vol_img2mip.m
 M cat_vol_slice_overlay.m


Changed: Many more changes to cat_surf_results.m, cat_vol_img2mip.m,
         cat_vol_slice_overlay.m to provide consistency
         between all displays.
------------------------------------------------------------------------
r2079 | gaser | 2022-08-10 15:15:09

Changed paths:
 M CHANGES.txt
 M cat_surf_results.m
 M cat_vol_img2mip.m
 M cat_vol_slice_overlay.m
 M slice_overlay.m


Changed: Many more changes to cat_surf_results.m, cat_vol_img2mip.m,
         cat_vol_slice_overlay.m and slice_overlay.m to provide consistency
         between all displays.
------------------------------------------------------------------------
r2078 | rdahnke | 2022-08-10 15:27:07

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m
 M cat_run.m


1) Fixed:    Tiny corrections in cat_run.
2) New:      Added imcalc batch to run the same operation on multiple subjects.
------------------------------------------------------------------------
r2077 | rdahnke | 2022-08-10 11:38:50

Changed paths:
 M .gitignore
 M CHANGES.txt
 M cat_parallelize.m
 M cat_run.m


1) New:    Added routine to keep some order with parallel processing log files.
           (i)  If BIDS is used then collect all parallel processing log files
                in a log subdirectory.
           (ii) If the current directory is located in the SPM path then try to
                the store parallel processing log files into a logs subdirectory
                in the cat12 main directory to avoid littering (also ignored by
                GitHub).
------------------------------------------------------------------------
r2076 | gaser | 2022-08-10 01:11:04

Changed paths:
 M CHANGES.txt
 M cat_surf_results.m
 M cat_vol_img2mip.m


Changed: Added option to leave slice definition empty in cat_surf_results.m
         to automatically estimate slices with local maxima.
------------------------------------------------------------------------
r2075 | gaser | 2022-08-10 00:19:02

Changed paths:
 M CHANGES.txt
 M cat_surf_results.m
 M cat_vol_img2mip.m
 M cat_vol_slice_overlay.m


Changed: Added option to skip display of colorbar in cat_vol_img2mip.m.
Changed: Changed function to save png-image in cat_vol_img2mip.m
Changed: Many changes in cat_surf_results:
           - close old windows if starting
           - corrected handling of OV.func
------------------------------------------------------------------------
r2074 | gaser | 2022-08-09 18:30:20

Changed paths:
 M CHANGES.txt
 M cat12.m
 M cat_stat_homogeneity.m
 M cat_surf_results.m
 M cat_vol_img2mip.m
 M cat_vol_slice_overlay.m
 M slice_overlay.m


Fixed:   Removed some smaller bugs in cat_stat_homogeneity.m.
Fixed:   Removed issues with colorbar and range in cat_surf_results.m.
Changed: Added option to control background color in cat_vol_slice_overlay.m
         and slice_overlay.m
Changed: Added option to control background color and added min/max text to
         single colorbar in cat_vol_img2mip.m.
Changed: Many changes in cat_surf_results:
           - added option to control background color
           - moved additional figure with slice control to main panel
           - corrected control of log-colorbar w.r.t. to cat_vol_slice_overlay.m
------------------------------------------------------------------------
r2073 | rdahnke | 2022-08-09 10:36:06

Changed paths:
 M CHANGES.txt
 M cat_main.m
 M cat_main1639.m
 M cat_run.m


1) Fixed:   Corrected stupid try-else bug in cat_main.
2) Fixed:   Corrected wrong file output of some maps in case of BIDS in cat_main[1639].
3) Fixed:   Corrected warning counter in parallel processing in cat_run.
------------------------------------------------------------------------
r2071 | gaser | 2022-08-08 17:32:54

Changed paths:
 M CHANGES.txt
 M cat_run_job1639.m
 M cat_stat_homogeneity.m
 M cat_surf_fun.m


Fixed: Removed some smaller bugs in cat_surf_fun.m, cat_stat_homogeneity.m
       and cat_run_job1639.m.
------------------------------------------------------------------------
r2070 | dahnke | 2022-08-08 12:25:59

Changed paths:
 M CHANGES.txt
 M cat_plot_boxplot.m
 M cat_tst_qa_cleaner.m
 M cat_vol_qa.m
A  cat_vol_qa202207b.m


1) Fixed:    Corrected bug in cat_plot_boxplot in case of small input data.
2) Fixed:    Corrected small bug in cat_vol_qa in case of failed processing.
------------------------------------------------------------------------
r2069 | rdahnke | 2022-08-08 11:20:36

Changed paths:
 M .gitignore
 M CHANGES.txt
 M cat_io_cprintf.m
 M cat_run.m


1) Fixed:   Corrected lazy processing of gzip-niftis.
2) Fixed:   Updated cat_io_cprintf by the current version of cprintf written by
            Yair M. Altman (altmany(at)gmail.com) distributed on Matlab central.
3) Changed: Added Matlab backup files *.asv to gitignore list.
------------------------------------------------------------------------
r2068 | rdahnke | 2022-08-08 09:50:05

Changed paths:
 M CHANGES.txt
 M cat_long_report.m
 M cat_main.m
 M cat_run.m
 M cat_vol_groupwise_ls.m
 M cat_vol_qa.m
 M cat_vol_series_align.m


1) Fixed:    Catching gunzip error in cat_run in case of alias (Datalad) files.
2) Changed:  Added another resampling test case in cat_vol_groupwise_ls.
3) Fixed:    Corrected tiny bug in cat_vol_series_align.
4) Fixed:    Remove temporary resampled surface files in cat_long_report.
5) Fixed:    Added another try-catch-block in cat_main_reportfig.
6) Fixed:    Corrected a bug in case cat_main_amap by calling the 1639 version.
7) Fixed:    Corrected reprocessing in cat_vol_qa.
------------------------------------------------------------------------
r2067 | rdahnke | 2022-08-07 11:18:32

Changed paths:
 M CHANGES.txt
 M cat_vol_resize.m


1) Changed:   Improved matrix balance in cat_vol_resize of low resolution cases.

------------------------------------------------------------------------
r2066 | gaser | 2022-08-03 16:41:23

Changed paths:
 M CHANGES.txt
 M cat_stat_homogeneity.m


Changed: Added option to show scatterplot and boxplot for additional covariates
         in cat_stat_homogeneity.m.
Changed: Many smaller changes to cat_stat_homogeneity.m to remove inconsistencies.
------------------------------------------------------------------------
r2065 | gaser | 2022-08-02 18:01:50

Changed paths:
 M CHANGES.txt
 M cat_conf_factorial.m
 M cat_main_reportfig.m
 M cat_run.m
 M cat_stat_check_SPM.m
 M cat_stat_homogeneity.m
 M cat_surf_display.m


Fixed:   Corrected handling of long. designs with one group in
         cat_conf_factorial.m.
Changed: Replaced flip command by flipud for compatibility reasons.
Changed: For long. designs subjects are now always displayed as separate
         boxplot in cat_stat_homogeneity.m.
Changed: Many changes to cat_stat_homogeneity.m to remove inconsistencies.
------------------------------------------------------------------------
r2064 | gaser | 2022-08-02 00:55:59

Changed paths:
 M CHANGES.txt
 M cat_stat_check_SPM.m
 M cat_stat_homogeneity.m


Changed: Disabled adjustment with design matrix for long. data in
         cat_stat_check_SPM.m
Changed: many changes to cat_stat_homogeneity.m:
         - Added colored connected lines to long. designs w.r.t. difference
           between time points.
         - Corrected image intensity in slice display.
         - Behaviour for removing data has changed.
------------------------------------------------------------------------
r2063 | gaser | 2022-08-01 12:01:11

Changed paths:
 M CHANGES.txt
 M cat_conf_factorial.m
 M cat_stat_check_SPM.m
 M cat_stat_homogeneity.m
 M cat_surf_render2.m
 M cat_surf_results.m
 M tbx_cfg_cat.m


Changed: Extended options for defining long. designs in cat_conf_factorial.m.
Changed: Some smaller changes for catching errors in cat_surf_results.m.
Changed: Chnaged position and size of render views in cat_stat_homogeneity.m.
Fixed:   Corrected wrong marker in cat_stat_homogeneity.m.
------------------------------------------------------------------------
r2062 | gaser | 2022-08-01 09:06:04

Changed paths:
 M CHANGES.txt
M  cat_stat_homogeneity.m


Added:   Corrected display of meshes for long. designs in
         cat_stat_homogeneity.m.
------------------------------------------------------------------------
r2061 | gaser | 2022-08-01 00:46:30

Changed paths:
 M CHANGES.txt
 M cat_conf_factorial.m
 M cat_stat_homogeneity.m
A  html/icons/file_cat_reportlong.png


Changed: Added handling of flexible factorial designs using 3 different
         definitions.
Changed: Added option for long. reports to cat_stat_homogeneity.m.
Fixed:   Corrected many smaller inconsistencies in cat_stat_homogeneity.m.
Added:   New icon for cat_stat_homogeneity.m.
------------------------------------------------------------------------
r2060 | gaser | 2022-07-31 01:52:32

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m
 M cat_long_report.m
 M cat_main_reportfig.m
 M cat_stat_check_SPM.m
 M cat_stat_homogeneity.m


Fixed:  Corrected incorrect entry for data_vol in cat_conf_tools.m.
Fixed:  Changed parameters in cat_main_reportfig according to new homogeneity
        function.
Fixed:  Corrected wrong indication og group factor in cat_stat_check_SPM.m
        for long. designs.
Fixed:  Solved some smaller issues in cat_stat_homogeneity.m.
------------------------------------------------------------------------
r2059 | gaser | 2022-07-29 23:01:03

Changed paths:
 M CHANGES.txt
 M Contents_info.txt
 M cat12.m
 M cat_conf_tools.m
 M cat_long_report.m
 M cat_stat_check_SPM.m
RM cat_stat_check_cov.m -> cat_stat_homogeneity.m
 D check_pipeline/IXI002-Guys-0828-T1.nii
 M check_pipeline/batch_surface_pipeline.m
 M check_pipeline/batch_volume_pipeline.m
 D check_pipeline/surf/lh.pbt.IXI002-Guys-0828-T1
 D check_pipeline/surf/lh.pbt.IXI016-Guys-0697-T1
 D check_pipeline/surf/lh.pbt.IXI017-Guys-0698-T1
 D check_pipeline/surf/lh.pbt.IXI019-Guys-0702-T1
 D check_pipeline/surf/rh.pbt.IXI002-Guys-0828-T1
 D check_pipeline/surf/rh.pbt.IXI016-Guys-0697-T1
 D check_pipeline/surf/rh.pbt.IXI017-Guys-0698-T1
 D check_pipeline/surf/rh.pbt.IXI019-Guys-0702-T1
 M check_pipeline_homogeneity.m


Changed: Renamed cat_stat_check_cov.m to cat_stat_homogeneity.m and changed all
         linked functions.------------------------------------------------------------------------
r2058 | gaser | 2022-07-29 22:27:11

Changed paths:
 M CHANGES.txt
 M cat_install_tfce.m
 M cat_stat_check_cov.m


Changed: Prepared cat_stat_check_cov.m to handle longitudinal data.
------------------------------------------------------------------------
r2057 | gaser | 2022-07-29 18:44:18

Changed paths:
 M CHANGES.txt
 M cat_conf_factorial.m
 M cat_conf_tools.m
 M cat_stat_check_cov.m


Fixed:   Corrected wrong parameter name in cat_conf_tools.m.
------------------------------------------------------------------------
r2056 | gaser | 2022-07-29 18:26:41

Changed paths:
 M CHANGES.txt
 M cat12.m
 M cat_conf_factorial.m
 M cat_conf_stools.m
 M cat_conf_tools.m
MM cat_stat_check_cov.m
D  cat_stat_check_cov2.m
AM cat_stat_check_cov_old.m
D  internal/cat_stat_check_SPM.m
R  cat_stat_factorial_design.m -> internal/cat_stat_factorial_design.m


Changed: Renamed original cat_stat_check_cov2.m to cat_stat_check_cov.m.
Changed: Updated all functions that call cat_stat_check_cov and removed this
         option for surfaces because this is now located in tools for both
         volumes and surfaces.
------------------------------------------------------------------------
r2055 | gaser | 2022-07-29 18:07:41

Changed paths:
 M CHANGES.txt
 M cat_conf_factorial.m
MM cat_stat_check_SPM.m
 M cat_stat_check_cov2.m
 M cat_stat_showslice_all.m
R  cat_stat_check_SPM2.m -> internal/cat_stat_check_SPM.m


Changed: Set group-specific AnCova as default for TIV correction in
         cat_conf_factorial.m.
Changed: Removed sone old options in cat_stat_showslice_all.m that are not
         needed anymore.
Changed: Many smaller changes to cat_stat_check_cov2.m to remove inconsitencies.
Changed: Prepared cat_stat_check_SPM.m for new z-score check.
------------------------------------------------------------------------
r2054 | gaser | 2022-07-28 17:43:44

Changed paths:
 M CHANGES.txt
 M cat_conf_factorial.m
A  cat_stat_check_SPM2.m
 M cat_stat_check_cov2.m


Changed: Prepared  factorial design to also allow check for sample homogeneity.
Changed: Added multiple regression and 2-sample t-test again to factorial
         design.
Added:   New tool for checking factorial designs.
------------------------------------------------------------------------
r2052 | gaser | 2022-07-28 01:40:04

Changed paths:
 M CHANGES.txt
A  html/icons/file_spm_view_p0.png


Changed: Added new icons for cat_stat_check_cov2.m
------------------------------------------------------------------------
r2051 | gaser | 2022-07-28 01:39:07

Changed paths:
 M CHANGES.txt
 M cat_conf_tools.m
 M cat_run.m
 M cat_run_job.m
 M cat_run_job1639.m
 M cat_stat_check_SPM.m
 M cat_stat_check_cov2.m
 M cat_stat_quality_measures.m
 M html/icons/file_spm_view.png


Fixed:   Corrected issue for zipped nii-files where name of log-file was
         not correct.
Changed: Updated cat_stat_check_cov2.m and linked functions.
Changed: Added new icons for cat_stat_check_cov2.m
------------------------------------------------------------------------
r2050 | gaser | 2022-07-26 18:14:47

Changed paths:
 M CHANGES.txt
A  html/icons/greenarrowicon.png
A  html/icons/list_del.png
A  html/icons/list_new.png
A  html/icons/tool_pointer.png


Changed: Added icons for cat_stat_check_cov2.m.
------------------------------------------------------------------------
r2049 | gaser | 2022-07-26 18:14:06

Changed paths:
 M CHANGES.txt
 M cat_conf_stools.m
 M cat_conf_tools.m
MM cat_stat_check_cov2.m
 M cat_surf_render.m
 M html/icons/tool_fit.png
R  cat_io_findjobj.m -> internal/cat_io_findjobj.m
A  internal/cat_stat_check_cov2.m


Changed: Moved old cat_stat_check_cov2.m version to internal folder.
Changed: Created new cat_stat_check_cov2.m that is based on mean z-score
         instead of mean correlation, which is much faster for larger samples.
Changed: Prepared cat_conf*.m for new cat_stat_check_cov2.m function.
Changed: Added and updated icons for cat_stat_check_cov2.m.
------------------------------------------------------------------------
r2048 | gaser | 2022-07-22 18:09:55

Changed paths:
 M .gitignore
 M CHANGES.txt
 M cat_stat_check_cov.m
 M cat_stat_quality_measures.m
 M cat_update.m
 M spm_cat12.m


Fixed:   Initializiation of isxml parameter in cat_stat_quality_measures.m.
Changed: Added zoom options and changed layout in cat_stat_check_cov.m.
Changed: Removed eval call from cat_update.m.
------------------------------------------------------------------------
r2046 | gaser | 2022-07-20 12:29:36

Changed paths:
 M .gitattributes
 M .gitignore
 M CHANGES.txt
A  templates_MNI152NLin2009cAsym_1mm/Template_0_GS1mm.nii
A  templates_MNI152NLin2009cAsym_1mm/Template_1_GS1mm.nii
A  templates_MNI152NLin2009cAsym_1mm/Template_2_GS1mm.nii
A  templates_MNI152NLin2009cAsym_1mm/Template_3_GS1mm.nii
A  templates_MNI152NLin2009cAsym_1mm/Template_4_GS1mm.nii


Added 1mm Geodesic Shooting templates.
------------------------------------------------------------------------
r2044 | gaser | 2022-07-20 12:24:32

Changed paths:
 M .gitattributes
 M CHANGES.txt
 M Contents.m
 M Makefile
 M html/cat.html


Added 1mm Geodesic Shooting templates.
------------------------------------------------------------------------
r2043 | gaser | 2022-07-20 11:49:22

Changed paths:
 M CHANGES.txt
 M Contents.m
 M Makefile
 M cat_update.m
 M html/cat.html
 M spm_cat12.m
 M update_revision.sh


1. Updated Makefile to consider new file structure
2. Fixed two issues in spm_cat12.m for open interactive help for newer Matlab
   versions and for dealing with mac permissions.
3. Some minor edits to cat_update.m and update_revision.sh
------------------------------------------------------------------------
r2041 | gaser | 2022-07-19 12:05:50

Changed paths:
 M CHANGES.txt
 M Contents.m
 M Makefile
 M html/cat.html


Updated Makefile
------------------------------------------------------------------------
r2037 | gaser | 2022-07-18 17:35:47

Changed paths:
 M CHANGES.txt
 M README.md


Updated README.md
------------------------------------------------------------------------
r2036 | gaser | 2022-07-18 17:34:48

Changed paths:
 M CHANGES.txt
 M README.md


Updated README.md
------------------------------------------------------------------------
r2035 | gaser | 2022-07-18 17:33:30

Changed paths:
 M CHANGES.txt
 M README.md


Updated README.md
------------------------------------------------------------------------
r2034 | gaser | 2022-07-18 17:26:39

Changed paths:
 M CHANGES.txt
A  README.md


Added README.md
------------------------------------------------------------------------
r2033 | gaser | 2022-07-18 17:24:57

Changed paths:
 M CHANGES.txt
 M html/cat.html


Added README.md
------------------------------------------------------------------------
r2032 | gaser | 2022-07-14 22:39:10

Changed paths:
 M CHANGES.txt


Fixed: Corrected capitals in some filenames in html/images.
------------------------------------------------------------------------
r2031 | gaser | 2022-07-14 22:03:49

Changed paths:
 M CHANGES.txt
 M cat_io_volctype.m
 M cat_long_createTPM.m
 M cat_parallelize.m
 M cat_spm_preproc_run.m
 M cat_spm_results_ui.m
 M cat_stat_getCSVXMLfield.m
 M cat_surf_display.m
 M cat_surf_parameters.m
 M cat_surf_resamp.m
 M cat_surf_smooth.m
 M cat_surf_vx2surf.m
 M cat_vol_display_label.m
 M cat_vol_headtrimming.m
 M cat_vol_imcalc.m
 M cat_vol_maskimage.m
 M cat_vol_sanlm.m
 M cat_vol_sanlm2.m
 M development/cat_stat_spm_results_ui.m


Removed SVNid and SVNrev from subversion.
------------------------------------------------------------------------
r2030 | dahnke | 2022-07-13 13:23:59

Changed paths:
 M .gitignore
 M CHANGES.txt
 M cat_surf_create_TPM_hull_surface.m


1) Fixed:     Corrected problem with headbrain mesh recreation. In case of
              an own TPM the mesh is written into the own TPM directory.

------------------------------------------------------------------------
r2029 | dahnke | 2022-07-13 12:08:28

Changed paths:
 M .gitignore
 M CHANGES.txt


1) Fixed:     Corrected a problem with own atlas maps saved as float
              rather than integer in cat_main_roi.
2) Fixed:     Create warning in cat_main_roi in case of atlas maps
              with positive x values that cannot be mapped via the used
              spm_sample_vol function. User has to provide images in
              the right orientation and space.
3) Fixed:     Use whole rather than natural numbers in cat_conf_tools to
              avoid opening of the input image in the head trimming tool.
4) Fixed:     Added checks in cat_run to detect incorrect named own atlases.

------------------------------------------------------------------------
r2024 | gaser | 2022-07-12 22:35:28

Updated website links
------------------------------------------------------------------------
r2022 | gaser | 2022-07-11 12:35:28

Changed paths:
 M CHANGES.txt

Added some HowTos for fMRI and PET.
------------------------------------------------------------------------
r2021 | gaser | 2022-07-11 12:26:37

Changed paths:
 M .gitignore
 M CHANGES.txt
 M Contents.m
 M Makefile
 M html/cat.html


Updated .gitignore.
Updated Makefile to consider new file structure.
------------------------------------------------------------------------
r2018 | gaser | 2022-07-07 16:38:42

Changed paths:
 M CHANGES.txt
 M Makefile
 M html/cat.html
 M html/cat.txt


Updated Makefile to copy cat12-html to another folder.
Updated html help text.
------------------------------------------------------------------------
r2017 | gaser | 2022-07-05 21:30:20

Changed paths:
 M CHANGES.txt
 M git_ci_log
 M standalone/cat_standalone.sh
 A standalone/cat_standalone_get_IQR.m


Updated git_ci_log and added -a flag to commit.
Added new option for getting image quality to cat_standalone.sh.
Added new function for getting image quality cat_standalone_get_IQR.m.
------------------------------------------------------------------------
r2016 | gaser | 2022-07-05 00:11:33

Changed paths:
 M .gitattributes
 M Amap.c
 M Bayes.c
 M BayesMex.c
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
 M Pve.c
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
 M cat_ornlm.c
 M cat_plot_circular.m
 M cat_sanlm.c
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
 M cat_vol_ROIval.c
 M cat_vol_downcut.c
 M cat_vol_eidist.c
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
 M cat_vol_gradient3.c
 M cat_vol_laplace3.c
 M cat_vol_laplace3R.c
 M cat_vol_localstat.c
 M cat_vol_median3.c
 M cat_vol_median3c.c
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
 M cat_vol_pbtp2.c
 M cat_vol_simgrow.c
 M cat_vol_smooth3X.m
 M check_pipeline_ROIs.m
 M genus0.c
M  git_ci_log
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
 M templates_MNI152NLin2009cAsym/hammers.txt
 M templates_volumes/hammers.txt

Updated git_ci_log
------------------------------------------------------------------------
r2015 | gaser | 2022-07-05 00:10:55

Changed paths:
 M .gitattributes
 M Amap.c
 M Bayes.c
 M BayesMex.c
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
 M Pve.c
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
 M cat_ornlm.c
 M cat_plot_circular.m
 M cat_sanlm.c
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
 M cat_vol_ROIval.c
 M cat_vol_downcut.c
 M cat_vol_eidist.c
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
 M cat_vol_gradient3.c
 M cat_vol_laplace3.c
 M cat_vol_laplace3R.c
 M cat_vol_localstat.c
 M cat_vol_median3.c
 M cat_vol_median3c.c
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
 M cat_vol_pbtp2.c
 M cat_vol_simgrow.c
 M cat_vol_smooth3X.m
 M check_pipeline_ROIs.m
 M genus0.c
 M git_ci_log
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
 M templates_MNI152NLin2009cAsym/hammers.txt
 M templates_volumes/hammers.txt

Updated git_ci_log
------------------------------------------------------------------------
r2015 | gaser | 2022-07-04 23:52:05

Changed paths:
 M .gitattributes
 M Amap.c
 M Bayes.c
 M BayesMex.c
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
 M Pve.c
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
 M cat_ornlm.c
 M cat_plot_circular.m
 M cat_sanlm.c
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
 M cat_vol_ROIval.c
 M cat_vol_downcut.c
 M cat_vol_eidist.c
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
 M cat_vol_gradient3.c
 M cat_vol_laplace3.c
 M cat_vol_laplace3R.c
 M cat_vol_localstat.c
 M cat_vol_median3.c
 M cat_vol_median3c.c
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
 M cat_vol_pbtp2.c
 M cat_vol_simgrow.c
 M cat_vol_smooth3X.m
 M check_pipeline_ROIs.m
 M genus0.c
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
 M templates_MNI152NLin2009cAsym/hammers.txt
 M templates_volumes/hammers.txt

Updated .gitattributes to remove files from Git LFS
------------------------------------------------------------------------
r2015 | gaser | 2022-07-04 23:49:48

Changed paths:
 M .gitattributes
 M Amap.c
 M Bayes.c
 M BayesMex.c
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
 M Pve.c
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
 M cat_ornlm.c
 M cat_plot_circular.m
 M cat_sanlm.c
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
 M cat_vol_ROIval.c
 M cat_vol_downcut.c
 M cat_vol_eidist.c
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
 M cat_vol_gradient3.c
 M cat_vol_laplace3.c
 M cat_vol_laplace3R.c
 M cat_vol_localstat.c
 M cat_vol_median3.c
 M cat_vol_median3c.c
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
 M cat_vol_pbtp2.c
 M cat_vol_simgrow.c
 M cat_vol_smooth3X.m
 M check_pipeline_ROIs.m
 M genus0.c
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
 M templates_MNI152NLin2009cAsym/hammers.txt
 M templates_volumes/hammers.txt

Updated .gitattributes to remove files from Git LFS
------------------------------------------------------------------------
r2014 | gaser | 2022-07-04 23:43:26

Changed paths:
 M .gitattributes
 M Amap.c
 M Bayes.c
 M BayesMex.c
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
 M Pve.c
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
 M cat_ornlm.c
 M cat_plot_circular.m
 M cat_sanlm.c
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
 M cat_vol_ROIval.c
 M cat_vol_downcut.c
 M cat_vol_eidist.c
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
 M cat_vol_gradient3.c
 M cat_vol_laplace3.c
 M cat_vol_laplace3R.c
 M cat_vol_localstat.c
 M cat_vol_median3.c
 M cat_vol_median3c.c
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
 M cat_vol_pbtp2.c
 M cat_vol_simgrow.c
 M cat_vol_smooth3X.m
 M check_pipeline_ROIs.m
 M genus0.c
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
 M templates_MNI152NLin2009cAsym/hammers.txt
A  templates_volumes/Schaefer2018_100Parcels_17Networks_order.nii
A  templates_volumes/Schaefer2018_200Parcels_17Networks_order.nii
A  templates_volumes/Schaefer2018_400Parcels_17Networks_order.nii
A  templates_volumes/Schaefer2018_600Parcels_17Networks_order.nii
A  templates_volumes/TPM_Age11.5.nii
A  templates_volumes/Template_0_IXI555_MNI152_GS.nii
A  templates_volumes/Template_1_IXI555_MNI152.nii
A  templates_volumes/Template_1_IXI555_MNI152_GS.nii
A  templates_volumes/Template_2_IXI555_MNI152.nii
A  templates_volumes/Template_2_IXI555_MNI152_GS.nii
A  templates_volumes/Template_3_IXI555_MNI152.nii
A  templates_volumes/Template_3_IXI555_MNI152_GS.nii
A  templates_volumes/Template_4_IXI555_MNI152.nii
A  templates_volumes/Template_4_IXI555_MNI152_GS.nii
A  templates_volumes/Template_5_IXI555_MNI152.nii
A  templates_volumes/Template_6_IXI555_MNI152.nii
A  templates_volumes/Template_T1_IXI555_MNI152_GS.nii
A  templates_volumes/aal3.nii
A  templates_volumes/anatomy3.nii
A  templates_volumes/brainmask.nii
A  templates_volumes/cat.nii
A  templates_volumes/cat_strokelesions_ATLAS303.nii
A  templates_volumes/cat_wmh.nii
A  templates_volumes/cat_wmh_miccai2017.nii
A  templates_volumes/cobra.nii
A  templates_volumes/hammers.nii
 M templates_volumes/hammers.txt
A  templates_volumes/ibsr.nii
A  templates_volumes/julichbrain.nii
A  templates_volumes/lpba40.nii
A  templates_volumes/mori.nii
A  templates_volumes/neuromorphometrics.nii

Updated .gitattributes to remove files from Git LFS
------------------------------------------------------------------------
r2014 | gaser | 2022-07-04 23:26:32

Changed paths:
 M .gitattributes
 M Amap.c
 M Bayes.c
 M BayesMex.c
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
 M Pve.c
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
 M cat_ornlm.c
 M cat_plot_circular.m
 M cat_sanlm.c
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
 M cat_vol_ROIval.c
 M cat_vol_downcut.c
 M cat_vol_eidist.c
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
 M cat_vol_gradient3.c
 M cat_vol_laplace3.c
 M cat_vol_laplace3R.c
 M cat_vol_localstat.c
 M cat_vol_median3.c
 M cat_vol_median3c.c
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
 M cat_vol_pbtp2.c
 M cat_vol_simgrow.c
 M cat_vol_smooth3X.m
 M check_pipeline_ROIs.m
 M genus0.c
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
 M templates_MNI152NLin2009cAsym/hammers.txt
 M templates_volumes/hammers.txt

Updated .gitattributes to remove files from Git LFS
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r2013 | gaser | 2022-07-04 23:18:42

Changed paths:
 M .gitattributes
 M Amap.c
 M Bayes.c
 M BayesMex.c
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
 M Pve.c
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
 M cat_ornlm.c
 M cat_plot_circular.m
 M cat_sanlm.c
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
 M cat_vol_ROIval.c
 M cat_vol_downcut.c
 M cat_vol_eidist.c
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
 M cat_vol_gradient3.c
 M cat_vol_laplace3.c
 M cat_vol_laplace3R.c
 M cat_vol_localstat.c
 M cat_vol_median3.c
 M cat_vol_median3c.c
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
 M cat_vol_pbtp2.c
 M cat_vol_simgrow.c
 M cat_vol_smooth3X.m
 M check_pipeline_ROIs.m
D  data/uint8_lowresR2x2x1_human_tumor_tp01.nii
D  data/uint8_lowresR2x2x2_primate_chimpanzee_laz.nii
D  data/uint8_lowresR2x2x2_primate_gibbon_gibbon4.nii
D  development/Template_0_GS1mm.nii
D  development/Template_0_IXI555_MNI152_GS1mm.nii
D  development/Template_1_GS1mm.nii
D  development/Template_1_IXI555_MNI152_GS1mm.nii
D  development/Template_2_GS1mm.nii
D  development/Template_2_IXI555_MNI152_GS1mm.nii
D  development/Template_3_GS1mm.nii
D  development/Template_3_IXI555_MNI152_GS1mm.nii
D  development/Template_4_GS1mm.nii
D  development/Template_4_IXI555_MNI152_GS1mm.nii
D  development/cat.nii
 M genus0.c
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
 M templates_MNI152NLin2009cAsym/hammers.txt
D  templates_animals/ape_greater_T1.nii
D  templates_animals/ape_greater_T2.nii
D  templates_animals/ape_greater_TPM.nii
D  templates_animals/ape_greater_TPMt.nii
D  templates_animals/ape_greater_Template_1.nii
D  templates_animals/ape_greater_Template_2.nii
D  templates_animals/ape_greater_Template_3.nii
D  templates_animals/ape_greater_Template_4.nii
D  templates_animals/ape_greater_Template_5.nii
D  templates_animals/ape_greater_Template_6.nii
D  templates_animals/ape_greater_brainmask.nii
D  templates_animals/ape_greater_cat.nii
D  templates_animals/baboon_T1.nii
D  templates_animals/baboon_TPM.nii
D  templates_animals/baboon_Template_1.nii
D  templates_animals/baboon_Template_2.nii
D  templates_animals/baboon_Template_3.nii
D  templates_animals/baboon_Template_4.nii
D  templates_animals/baboon_Template_5.nii
D  templates_animals/baboon_Template_6.nii
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D  templates_animals/baboon_cat.nii
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D  templates_animals/chimpanzee_Template_0_GS.nii
D  templates_animals/chimpanzee_Template_1_GS.nii
D  templates_animals/chimpanzee_Template_2_GS.nii
D  templates_animals/chimpanzee_Template_3_GS.nii
D  templates_animals/chimpanzee_Template_4_GS.nii
D  templates_animals/chimpanzee_atlas_davi.nii
D  templates_animals/chimpanzee_brainmask.nii
D  templates_animals/chimpanzee_cat.nii
D  templates_animals/dog_T1.nii
D  templates_animals/dog_Template_0.nii
D  templates_animals/dog_Template_1.nii
D  templates_animals/dog_Template_2.nii
D  templates_animals/dog_Template_3.nii
D  templates_animals/dog_Template_4.nii
D  templates_animals/dog_Template_5.nii
D  templates_animals/dog_Template_6.nii
D  templates_animals/dog_brainmask.nii
D  templates_animals/monkey_oldworld_T1.nii
D  templates_animals/monkey_oldworld_T2.nii
D  templates_animals/monkey_oldworld_TPM.nii
D  templates_animals/monkey_oldworld_Template_1.nii
D  templates_animals/monkey_oldworld_Template_2.nii
D  templates_animals/monkey_oldworld_Template_3.nii
D  templates_animals/monkey_oldworld_Template_4.nii
D  templates_animals/monkey_oldworld_Template_5.nii
D  templates_animals/monkey_oldworld_Template_6.nii
D  templates_animals/monkey_oldworld_atlas_inia19NeuroMaps.nii
D  templates_animals/monkey_oldworld_brainmask.nii
D  templates_animals/monkey_oldworld_cat.nii
D  templates_external/MNI152NLin2009cAsym.nii
D  templates_external/MNI152NLin2009cSym.nii
D  templates_external/MNI152NLin6Asym.nii
D  templates_external/MNIColin27.nii
D  templates_external/y_IXI555Dartel_to_MNI152NLin2009cAsym.nii
D  templates_external/y_MNI152NLin2009cSym_to_MNI152NLin2009cAsym.nii
D  templates_external/y_MNI152NLin6Asym_to_MNI152NLin2009cAsym.nii
D  templates_external/y_MNIColin27_to_MNI152NLin2009cAsym.nii
D  templates_external/y_fMNI152NLin2009cAsym_to_MNI152NLin2009cAsym.nii
D  templates_volumes/Schaefer2018_100Parcels_17Networks_order.nii
D  templates_volumes/Schaefer2018_200Parcels_17Networks_order.nii
D  templates_volumes/Schaefer2018_400Parcels_17Networks_order.nii
D  templates_volumes/Schaefer2018_600Parcels_17Networks_order.nii
D  templates_volumes/TPM_Age11.5.nii
D  templates_volumes/Template_0_IXI555_MNI152_GS.nii
D  templates_volumes/Template_1_IXI555_MNI152.nii
D  templates_volumes/Template_1_IXI555_MNI152_GS.nii
D  templates_volumes/Template_2_IXI555_MNI152.nii
D  templates_volumes/Template_2_IXI555_MNI152_GS.nii
D  templates_volumes/Template_3_IXI555_MNI152.nii
D  templates_volumes/Template_3_IXI555_MNI152_GS.nii
D  templates_volumes/Template_4_IXI555_MNI152.nii
D  templates_volumes/Template_4_IXI555_MNI152_GS.nii
D  templates_volumes/Template_5_IXI555_MNI152.nii
D  templates_volumes/Template_6_IXI555_MNI152.nii
D  templates_volumes/Template_T1_IXI555_MNI152_GS.nii
D  templates_volumes/aal3.nii
D  templates_volumes/anatomy3.nii
D  templates_volumes/brainmask.nii
D  templates_volumes/cat.nii
D  templates_volumes/cat_strokelesions_ATLAS303.nii
D  templates_volumes/cat_wmh.nii
D  templates_volumes/cat_wmh_miccai2017.nii
D  templates_volumes/cobra.nii
D  templates_volumes/hammers.nii
 M templates_volumes/hammers.txt
D  templates_volumes/ibsr.nii
D  templates_volumes/julichbrain.nii
D  templates_volumes/lpba40.nii
D  templates_volumes/mori.nii
D  templates_volumes/neuromorphometrics.nii
D  templates_volumes_not_distributed/aal.nii
D  templates_volumes_not_distributed/anatomy.nii
D  templates_volumes_not_distributed/aparc_DKT40.nii
D  templates_volumes_not_distributed/aparc_a2009s.nii

Removed some large files from Git Large File Storage because size exceeded 1GB

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r2012 | gaser | 2022-07-04 22:52:20

Changed paths:
AM .gitattributes
 M Amap.c
 M Bayes.c
 M BayesMex.c
A  CAT.glnx86/CAT_3dVol2Surf
A  CAT.glnx86/CAT_AddValuesToSurf
A  CAT.glnx86/CAT_AverageSurfaces
A  CAT.glnx86/CAT_BlurSurfHK
A  CAT.glnx86/CAT_Central2Pial
A  CAT.glnx86/CAT_DeformSurf
A  CAT.glnx86/CAT_DumpCurv
A  CAT.glnx86/CAT_DumpSurfArea
A  CAT.glnx86/CAT_DumpSurfaceRatio
A  CAT.glnx86/CAT_FixTopology
A  CAT.glnx86/CAT_FractalDimension
A  CAT.glnx86/CAT_Hausdorff
A  CAT.glnx86/CAT_Isometize
A  CAT.glnx86/CAT_MarkDefects
A  CAT.glnx86/CAT_RefineMesh
A  CAT.glnx86/CAT_ResampleSphericalSurf
A  CAT.glnx86/CAT_ResampleSphericalSurfSPH
A  CAT.glnx86/CAT_ResampleSurf
A  CAT.glnx86/CAT_SelfIntersect
A  CAT.glnx86/CAT_SeparatePolygon
A  CAT.glnx86/CAT_SmoothConvexity
A  CAT.glnx86/CAT_SulcusDepth
A  CAT.glnx86/CAT_Surf2Sphere
A  CAT.glnx86/CAT_Surf2Vol
A  CAT.glnx86/CAT_SurfDistance
A  CAT.glnx86/CAT_WarpSurf
A  CAT.maca64/CAT_3dVol2Surf
A  CAT.maca64/CAT_AddValuesToSurf
A  CAT.maca64/CAT_AverageSurfaces
A  CAT.maca64/CAT_BlurSurfHK
A  CAT.maca64/CAT_Central2Pial
A  CAT.maca64/CAT_DeformSurf
A  CAT.maca64/CAT_DumpCurv
A  CAT.maca64/CAT_DumpSurfArea
A  CAT.maca64/CAT_DumpSurfaceRatio
A  CAT.maca64/CAT_FixTopology
A  CAT.maca64/CAT_FractalDimension
A  CAT.maca64/CAT_Hausdorff
A  CAT.maca64/CAT_Isometize
A  CAT.maca64/CAT_MarkDefects
A  CAT.maca64/CAT_RefineMesh
A  CAT.maca64/CAT_ResampleSphericalSurf
A  CAT.maca64/CAT_ResampleSphericalSurfSPH
A  CAT.maca64/CAT_ResampleSurf
A  CAT.maca64/CAT_SelfIntersect
A  CAT.maca64/CAT_SeparatePolygon
A  CAT.maca64/CAT_SmoothConvexity
A  CAT.maca64/CAT_SulcusDepth
A  CAT.maca64/CAT_Surf2Sphere
A  CAT.maca64/CAT_Surf2Vol
A  CAT.maca64/CAT_SurfDistance
A  CAT.maca64/CAT_WarpSurf
A  CAT.maci64/CAT_3dVol2Surf
A  CAT.maci64/CAT_AddValuesToSurf
A  CAT.maci64/CAT_AverageSurfaces
A  CAT.maci64/CAT_BlurSurfHK
A  CAT.maci64/CAT_Central2Pial
A  CAT.maci64/CAT_DeformSurf
A  CAT.maci64/CAT_DumpCurv
A  CAT.maci64/CAT_DumpSurfArea
A  CAT.maci64/CAT_DumpSurfaceRatio
A  CAT.maci64/CAT_FixTopology
A  CAT.maci64/CAT_FractalDimension
A  CAT.maci64/CAT_Hausdorff
A  CAT.maci64/CAT_Isometize
A  CAT.maci64/CAT_MarkDefects
A  CAT.maci64/CAT_RefineMesh
A  CAT.maci64/CAT_ResampleSphericalSurf
A  CAT.maci64/CAT_ResampleSphericalSurfSPH
A  CAT.maci64/CAT_ResampleSurf
A  CAT.maci64/CAT_SelfIntersect
A  CAT.maci64/CAT_SeparatePolygon
A  CAT.maci64/CAT_SmoothConvexity
A  CAT.maci64/CAT_SulcusDepth
A  CAT.maci64/CAT_Surf2Sphere
A  CAT.maci64/CAT_Surf2Vol
A  CAT.maci64/CAT_SurfDistance
A  CAT.maci64/CAT_WarpSurf
A  CAT.w32/CAT_3dVol2Surf.exe
A  CAT.w32/CAT_AddValuesToSurf.exe
A  CAT.w32/CAT_AverageSurfaces.exe
A  CAT.w32/CAT_BlurSurfHK.exe
A  CAT.w32/CAT_Central2Pial.exe
A  CAT.w32/CAT_DeformSurf.exe
A  CAT.w32/CAT_DumpCurv.exe
A  CAT.w32/CAT_DumpSurfArea.exe
A  CAT.w32/CAT_DumpSurfaceRatio.exe
A  CAT.w32/CAT_FixTopology.exe
A  CAT.w32/CAT_FractalDimension.exe
A  CAT.w32/CAT_Hausdorff.exe
A  CAT.w32/CAT_Isometize.exe
A  CAT.w32/CAT_MarkDefects.exe
A  CAT.w32/CAT_RefineMesh.exe
A  CAT.w32/CAT_ResampleSphericalSurf.exe
A  CAT.w32/CAT_ResampleSphericalSurfSPH.exe
A  CAT.w32/CAT_ResampleSurf.exe
A  CAT.w32/CAT_SelfIntersect.exe
A  CAT.w32/CAT_SeparatePolygon.exe
A  CAT.w32/CAT_SmoothConvexity.exe
A  CAT.w32/CAT_SulcusDepth.exe
A  CAT.w32/CAT_Surf2Sphere.exe
A  CAT.w32/CAT_Surf2Vol.exe
A  CAT.w32/CAT_SurfDistance.exe
A  CAT.w32/CAT_WarpSurf.exe
A  CAT12-Manual-Word-Old.docx
A  CAT12-Manual.pdf
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
A  OverlayCAT12_cg.docx
 M Pve.c
A  VBM12-Manual_Japanese.doc
A  VBM12-Manual_Japanese.pdf
A  VBM8-flowchart.doc
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
 M cat_ornlm.c
 M cat_plot_circular.m
 M cat_sanlm.c
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
 M cat_vol_ROIval.c
 M cat_vol_downcut.c
 M cat_vol_eidist.c
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
 M cat_vol_gradient3.c
 M cat_vol_laplace3.c
 M cat_vol_laplace3R.c
 M cat_vol_localstat.c
 M cat_vol_median3.c
 M cat_vol_median3c.c
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
 M cat_vol_pbtp2.c
 M cat_vol_simgrow.c
 M cat_vol_smooth3X.m
A  check_pipeline/IXI002-Guys-0828-T1.nii
 M check_pipeline_ROIs.m
A  data/uint8_lowresR2x2x1_human_tumor_tp01.nii
A  data/uint8_lowresR2x2x2_primate_chimpanzee_laz.nii
A  data/uint8_lowresR2x2x2_primate_gibbon_gibbon4.nii
M  development/Template_0_GS1mm.nii
A  development/Template_0_IXI555_MNI152_GS1mm.nii
M  development/Template_1_GS1mm.nii
A  development/Template_1_IXI555_MNI152_GS1mm.nii
M  development/Template_2_GS1mm.nii
A  development/Template_2_IXI555_MNI152_GS1mm.nii
M  development/Template_3_GS1mm.nii
A  development/Template_3_IXI555_MNI152_GS1mm.nii
M  development/Template_4_GS1mm.nii
A  development/Template_4_IXI555_MNI152_GS1mm.nii
A  development/cat.nii
 M genus0.c
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
M  templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii
M  templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii
M  templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii
M  templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii
M  templates_MNI152NLin2009cAsym/T1.nii
M  templates_MNI152NLin2009cAsym/TPM_Age11.5.nii
M  templates_MNI152NLin2009cAsym/Template_0_GS.nii
M  templates_MNI152NLin2009cAsym/Template_1_Dartel.nii
M  templates_MNI152NLin2009cAsym/Template_1_GS.nii
M  templates_MNI152NLin2009cAsym/Template_2_Dartel.nii
M  templates_MNI152NLin2009cAsym/Template_2_GS.nii
M  templates_MNI152NLin2009cAsym/Template_3_Dartel.nii
M  templates_MNI152NLin2009cAsym/Template_3_GS.nii
M  templates_MNI152NLin2009cAsym/Template_4_Dartel.nii
M  templates_MNI152NLin2009cAsym/Template_4_GS.nii
M  templates_MNI152NLin2009cAsym/Template_5_Dartel.nii
M  templates_MNI152NLin2009cAsym/Template_6_Dartel.nii
M  templates_MNI152NLin2009cAsym/Template_T1.nii
M  templates_MNI152NLin2009cAsym/Template_T1_masked.nii
M  templates_MNI152NLin2009cAsym/aal3.nii
M  templates_MNI152NLin2009cAsym/anatomy3.nii
M  templates_MNI152NLin2009cAsym/brainmask.nii
M  templates_MNI152NLin2009cAsym/brainmask_T1.nii
M  templates_MNI152NLin2009cAsym/cat.nii
M  templates_MNI152NLin2009cAsym/cat_1mm.nii
M  templates_MNI152NLin2009cAsym/cat_strokelesions_ATLAS303.nii
M  templates_MNI152NLin2009cAsym/cat_wmh.nii
M  templates_MNI152NLin2009cAsym/cat_wmh_miccai2017.nii
M  templates_MNI152NLin2009cAsym/cobra.nii
M  templates_MNI152NLin2009cAsym/hammers.nii
 M templates_MNI152NLin2009cAsym/hammers.txt
M  templates_MNI152NLin2009cAsym/ibsr.nii
M  templates_MNI152NLin2009cAsym/julichbrain.nii
M  templates_MNI152NLin2009cAsym/lpba40.nii
M  templates_MNI152NLin2009cAsym/mori.nii
M  templates_MNI152NLin2009cAsym/neuromorphometrics.nii
M  templates_MNI152NLin2009cAsym/suit.nii
M  templates_MNI152NLin2009cAsym/thalamus.nii
A  templates_animals/ape_greater_T1.nii
A  templates_animals/ape_greater_T2.nii
A  templates_animals/ape_greater_TPM.nii
A  templates_animals/ape_greater_TPMt.nii
A  templates_animals/ape_greater_Template_1.nii
A  templates_animals/ape_greater_Template_2.nii
A  templates_animals/ape_greater_Template_3.nii
A  templates_animals/ape_greater_Template_4.nii
A  templates_animals/ape_greater_Template_5.nii
A  templates_animals/ape_greater_Template_6.nii
A  templates_animals/ape_greater_brainmask.nii
A  templates_animals/ape_greater_cat.nii
A  templates_animals/baboon_T1.nii
A  templates_animals/baboon_TPM.nii
A  templates_animals/baboon_Template_1.nii
A  templates_animals/baboon_Template_2.nii
A  templates_animals/baboon_Template_3.nii
A  templates_animals/baboon_Template_4.nii
A  templates_animals/baboon_Template_5.nii
A  templates_animals/baboon_Template_6.nii
A  templates_animals/baboon_brainmask.nii
A  templates_animals/baboon_cat.nii
A  templates_animals/chimpanzee_T1.nii
A  templates_animals/chimpanzee_TPM.nii
A  templates_animals/chimpanzee_Template_0_GS.nii
A  templates_animals/chimpanzee_Template_1_GS.nii
A  templates_animals/chimpanzee_Template_2_GS.nii
A  templates_animals/chimpanzee_Template_3_GS.nii
A  templates_animals/chimpanzee_Template_4_GS.nii
A  templates_animals/chimpanzee_atlas_davi.nii
A  templates_animals/chimpanzee_brainmask.nii
A  templates_animals/chimpanzee_cat.nii
A  templates_animals/dog_T1.nii
A  templates_animals/dog_Template_0.nii
A  templates_animals/dog_Template_1.nii
A  templates_animals/dog_Template_2.nii
A  templates_animals/dog_Template_3.nii
A  templates_animals/dog_Template_4.nii
A  templates_animals/dog_Template_5.nii
A  templates_animals/dog_Template_6.nii
A  templates_animals/dog_brainmask.nii
A  templates_animals/monkey_oldworld_T1.nii
A  templates_animals/monkey_oldworld_T2.nii
A  templates_animals/monkey_oldworld_TPM.nii
A  templates_animals/monkey_oldworld_Template_1.nii
A  templates_animals/monkey_oldworld_Template_2.nii
A  templates_animals/monkey_oldworld_Template_3.nii
A  templates_animals/monkey_oldworld_Template_4.nii
A  templates_animals/monkey_oldworld_Template_5.nii
A  templates_animals/monkey_oldworld_Template_6.nii
A  templates_animals/monkey_oldworld_atlas_inia19NeuroMaps.nii
A  templates_animals/monkey_oldworld_brainmask.nii
A  templates_animals/monkey_oldworld_cat.nii
A  templates_external/MNI152NLin2009cAsym.nii
A  templates_external/MNI152NLin2009cSym.nii
A  templates_external/MNI152NLin6Asym.nii
A  templates_external/MNIColin27.nii
A  templates_external/y_IXI555Dartel_to_MNI152NLin2009cAsym.nii
A  templates_external/y_MNI152NLin2009cSym_to_MNI152NLin2009cAsym.nii
A  templates_external/y_MNI152NLin6Asym_to_MNI152NLin2009cAsym.nii
A  templates_external/y_MNIColin27_to_MNI152NLin2009cAsym.nii
A  templates_external/y_fMNI152NLin2009cAsym_to_MNI152NLin2009cAsym.nii
A  templates_volumes/Schaefer2018_100Parcels_17Networks_order.nii
A  templates_volumes/Schaefer2018_200Parcels_17Networks_order.nii
A  templates_volumes/Schaefer2018_400Parcels_17Networks_order.nii
A  templates_volumes/Schaefer2018_600Parcels_17Networks_order.nii
A  templates_volumes/TPM_Age11.5.nii
A  templates_volumes/Template_0_IXI555_MNI152_GS.nii
A  templates_volumes/Template_1_IXI555_MNI152.nii
A  templates_volumes/Template_1_IXI555_MNI152_GS.nii
A  templates_volumes/Template_2_IXI555_MNI152.nii
A  templates_volumes/Template_2_IXI555_MNI152_GS.nii
A  templates_volumes/Template_3_IXI555_MNI152.nii
A  templates_volumes/Template_3_IXI555_MNI152_GS.nii
A  templates_volumes/Template_4_IXI555_MNI152.nii
A  templates_volumes/Template_4_IXI555_MNI152_GS.nii
A  templates_volumes/Template_5_IXI555_MNI152.nii
A  templates_volumes/Template_6_IXI555_MNI152.nii
A  templates_volumes/Template_T1_IXI555_MNI152_GS.nii
A  templates_volumes/aal3.nii
A  templates_volumes/anatomy3.nii
A  templates_volumes/brainmask.nii
A  templates_volumes/cat.nii
A  templates_volumes/cat_strokelesions_ATLAS303.nii
A  templates_volumes/cat_wmh.nii
A  templates_volumes/cat_wmh_miccai2017.nii
A  templates_volumes/cobra.nii
A  templates_volumes/hammers.nii
 M templates_volumes/hammers.txt
A  templates_volumes/ibsr.nii
A  templates_volumes/julichbrain.nii
A  templates_volumes/lpba40.nii
A  templates_volumes/mori.nii
A  templates_volumes/neuromorphometrics.nii
A  templates_volumes_not_distributed/aal.nii
A  templates_volumes_not_distributed/anatomy.nii
A  templates_volumes_not_distributed/aparc_DKT40.nii
A  templates_volumes_not_distributed/aparc_a2009s.nii

Moved large files to Git Large File Storage

------------------------------------------------------------------------
r2011 | gaser | 2022-07-04 22:41:33

Changed paths:
 M Amap.c
 M Bayes.c
 M BayesMex.c
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
 M Pve.c
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
 M cat_ornlm.c
 M cat_plot_circular.m
 M cat_sanlm.c
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
 M cat_vol_ROIval.c
 M cat_vol_downcut.c
 M cat_vol_eidist.c
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
 M cat_vol_gradient3.c
 M cat_vol_laplace3.c
 M cat_vol_laplace3R.c
 M cat_vol_localstat.c
 M cat_vol_median3.c
 M cat_vol_median3c.c
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
 M cat_vol_pbtp2.c
 M cat_vol_simgrow.c
 M cat_vol_smooth3X.m
 M check_pipeline_ROIs.m
A  development/Template_0_GS1mm.nii
A  development/Template_1_GS1mm.nii
A  development/Template_2_GS1mm.nii
A  development/Template_3_GS1mm.nii
A  development/Template_4_GS1mm.nii
 M genus0.c
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
 M templates_MNI152NLin2009cAsym/hammers.txt
 M templates_volumes/hammers.txt

Added 1mm Shooting templates

------------------------------------------------------------------------
r2010 | gaser | 2022-07-04 22:23:42

Changed paths:
 M Amap.c
 M Bayes.c
 M BayesMex.c
D  CAT.glnx86/CAT_3dVol2Surf
D  CAT.glnx86/CAT_AddValuesToSurf
D  CAT.glnx86/CAT_AverageSurfaces
D  CAT.glnx86/CAT_BlurSurfHK
D  CAT.glnx86/CAT_Central2Pial
D  CAT.glnx86/CAT_DeformSurf
D  CAT.glnx86/CAT_DumpCurv
D  CAT.glnx86/CAT_DumpSurfArea
D  CAT.glnx86/CAT_DumpSurfaceRatio
D  CAT.glnx86/CAT_FixTopology
D  CAT.glnx86/CAT_FractalDimension
D  CAT.glnx86/CAT_Hausdorff
D  CAT.glnx86/CAT_Isometize
D  CAT.glnx86/CAT_MarkDefects
D  CAT.glnx86/CAT_RefineMesh
D  CAT.glnx86/CAT_ResampleSphericalSurf
D  CAT.glnx86/CAT_ResampleSphericalSurfSPH
D  CAT.glnx86/CAT_ResampleSurf
D  CAT.glnx86/CAT_SelfIntersect
D  CAT.glnx86/CAT_SeparatePolygon
D  CAT.glnx86/CAT_SmoothConvexity
D  CAT.glnx86/CAT_SulcusDepth
D  CAT.glnx86/CAT_Surf2Sphere
D  CAT.glnx86/CAT_Surf2Vol
D  CAT.glnx86/CAT_SurfDistance
D  CAT.glnx86/CAT_WarpSurf
D  CAT.maca64/CAT_3dVol2Surf
D  CAT.maca64/CAT_AddValuesToSurf
D  CAT.maca64/CAT_AverageSurfaces
D  CAT.maca64/CAT_BlurSurfHK
D  CAT.maca64/CAT_Central2Pial
D  CAT.maca64/CAT_DeformSurf
D  CAT.maca64/CAT_DumpCurv
D  CAT.maca64/CAT_DumpSurfArea
D  CAT.maca64/CAT_DumpSurfaceRatio
D  CAT.maca64/CAT_FixTopology
D  CAT.maca64/CAT_FractalDimension
D  CAT.maca64/CAT_Hausdorff
D  CAT.maca64/CAT_Isometize
D  CAT.maca64/CAT_MarkDefects
D  CAT.maca64/CAT_RefineMesh
D  CAT.maca64/CAT_ResampleSphericalSurf
D  CAT.maca64/CAT_ResampleSphericalSurfSPH
D  CAT.maca64/CAT_ResampleSurf
D  CAT.maca64/CAT_SelfIntersect
D  CAT.maca64/CAT_SeparatePolygon
D  CAT.maca64/CAT_SmoothConvexity
D  CAT.maca64/CAT_SulcusDepth
D  CAT.maca64/CAT_Surf2Sphere
D  CAT.maca64/CAT_Surf2Vol
D  CAT.maca64/CAT_SurfDistance
D  CAT.maca64/CAT_WarpSurf
D  CAT.maci64/CAT_3dVol2Surf
D  CAT.maci64/CAT_AddValuesToSurf
D  CAT.maci64/CAT_AverageSurfaces
D  CAT.maci64/CAT_BlurSurfHK
D  CAT.maci64/CAT_Central2Pial
D  CAT.maci64/CAT_DeformSurf
D  CAT.maci64/CAT_DumpCurv
D  CAT.maci64/CAT_DumpSurfArea
D  CAT.maci64/CAT_DumpSurfaceRatio
D  CAT.maci64/CAT_FixTopology
D  CAT.maci64/CAT_FractalDimension
D  CAT.maci64/CAT_Hausdorff
D  CAT.maci64/CAT_Isometize
D  CAT.maci64/CAT_MarkDefects
D  CAT.maci64/CAT_RefineMesh
D  CAT.maci64/CAT_ResampleSphericalSurf
D  CAT.maci64/CAT_ResampleSphericalSurfSPH
D  CAT.maci64/CAT_ResampleSurf
D  CAT.maci64/CAT_SelfIntersect
D  CAT.maci64/CAT_SeparatePolygon
D  CAT.maci64/CAT_SmoothConvexity
D  CAT.maci64/CAT_SulcusDepth
D  CAT.maci64/CAT_Surf2Sphere
D  CAT.maci64/CAT_Surf2Vol
D  CAT.maci64/CAT_SurfDistance
D  CAT.maci64/CAT_WarpSurf
D  CAT.w32/CAT_3dVol2Surf.exe
D  CAT.w32/CAT_AddValuesToSurf.exe
D  CAT.w32/CAT_AverageSurfaces.exe
D  CAT.w32/CAT_BlurSurfHK.exe
D  CAT.w32/CAT_Central2Pial.exe
D  CAT.w32/CAT_DeformSurf.exe
D  CAT.w32/CAT_DumpCurv.exe
D  CAT.w32/CAT_DumpSurfArea.exe
D  CAT.w32/CAT_DumpSurfaceRatio.exe
D  CAT.w32/CAT_FixTopology.exe
D  CAT.w32/CAT_FractalDimension.exe
D  CAT.w32/CAT_Hausdorff.exe
D  CAT.w32/CAT_Isometize.exe
D  CAT.w32/CAT_MarkDefects.exe
D  CAT.w32/CAT_RefineMesh.exe
D  CAT.w32/CAT_ResampleSphericalSurf.exe
D  CAT.w32/CAT_ResampleSphericalSurfSPH.exe
D  CAT.w32/CAT_ResampleSurf.exe
D  CAT.w32/CAT_SelfIntersect.exe
D  CAT.w32/CAT_SeparatePolygon.exe
D  CAT.w32/CAT_SmoothConvexity.exe
D  CAT.w32/CAT_SulcusDepth.exe
D  CAT.w32/CAT_Surf2Sphere.exe
D  CAT.w32/CAT_Surf2Vol.exe
D  CAT.w32/CAT_SurfDistance.exe
D  CAT.w32/CAT_WarpSurf.exe
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
 M Pve.c
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
 M cat_ornlm.c
 M cat_plot_circular.m
 M cat_sanlm.c
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
 M cat_vol_ROIval.c
 M cat_vol_downcut.c
 M cat_vol_eidist.c
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
 M cat_vol_gradient3.c
 M cat_vol_laplace3.c
 M cat_vol_laplace3R.c
 M cat_vol_localstat.c
 M cat_vol_median3.c
 M cat_vol_median3c.c
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
 M cat_vol_pbtp2.c
 M cat_vol_simgrow.c
 M cat_vol_smooth3X.m
 M check_pipeline_ROIs.m
 M genus0.c
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
A  templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii
A  templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii
A  templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii
A  templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii
A  templates_MNI152NLin2009cAsym/T1.nii
A  templates_MNI152NLin2009cAsym/TPM_Age11.5.nii
A  templates_MNI152NLin2009cAsym/Template_0_GS.nii
A  templates_MNI152NLin2009cAsym/Template_1_Dartel.nii
A  templates_MNI152NLin2009cAsym/Template_1_GS.nii
A  templates_MNI152NLin2009cAsym/Template_2_Dartel.nii
A  templates_MNI152NLin2009cAsym/Template_2_GS.nii
A  templates_MNI152NLin2009cAsym/Template_3_Dartel.nii
A  templates_MNI152NLin2009cAsym/Template_3_GS.nii
A  templates_MNI152NLin2009cAsym/Template_4_Dartel.nii
A  templates_MNI152NLin2009cAsym/Template_4_GS.nii
A  templates_MNI152NLin2009cAsym/Template_5_Dartel.nii
A  templates_MNI152NLin2009cAsym/Template_6_Dartel.nii
A  templates_MNI152NLin2009cAsym/Template_T1.nii
A  templates_MNI152NLin2009cAsym/Template_T1_masked.nii
A  templates_MNI152NLin2009cAsym/aal3.nii
A  templates_MNI152NLin2009cAsym/anatomy3.nii
A  templates_MNI152NLin2009cAsym/brainmask.nii
A  templates_MNI152NLin2009cAsym/brainmask_T1.nii
A  templates_MNI152NLin2009cAsym/cat.nii
A  templates_MNI152NLin2009cAsym/cat_1mm.nii
A  templates_MNI152NLin2009cAsym/cat_strokelesions_ATLAS303.nii
A  templates_MNI152NLin2009cAsym/cat_wmh.nii
A  templates_MNI152NLin2009cAsym/cat_wmh_miccai2017.nii
A  templates_MNI152NLin2009cAsym/cobra.nii
A  templates_MNI152NLin2009cAsym/hammers.nii
 M templates_MNI152NLin2009cAsym/hammers.txt
A  templates_MNI152NLin2009cAsym/ibsr.nii
A  templates_MNI152NLin2009cAsym/julichbrain.nii
A  templates_MNI152NLin2009cAsym/lpba40.nii
A  templates_MNI152NLin2009cAsym/mori.nii
A  templates_MNI152NLin2009cAsym/neuromorphometrics.nii
A  templates_MNI152NLin2009cAsym/suit.nii
A  templates_MNI152NLin2009cAsym/thalamus.nii
 M templates_volumes/hammers.txt

Added *.nii files again

------------------------------------------------------------------------
r2009 | gaser | 2022-07-04 22:13:35

Changed paths:
 M Amap.c
 M Bayes.c
 M BayesMex.c
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
 M Pve.c
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
 M cat_ornlm.c
 M cat_plot_circular.m
 M cat_sanlm.c
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
 M cat_vol_ROIval.c
 M cat_vol_downcut.c
 M cat_vol_eidist.c
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
 M cat_vol_gradient3.c
 M cat_vol_laplace3.c
 M cat_vol_laplace3R.c
 M cat_vol_localstat.c
 M cat_vol_median3.c
 M cat_vol_median3c.c
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
 M cat_vol_pbtp2.c
 M cat_vol_simgrow.c
 M cat_vol_smooth3X.m
 M check_pipeline_ROIs.m
 M genus0.c
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
 M templates_MNI152NLin2009cAsym/hammers.txt
A  templates_animals_surfaces/bh.headbrain.ape_greater_TPM.gii
A  templates_animals_surfaces/bh.headbrain.chimpanzee_TPM.gii
A  templates_animals_surfaces/bh.headbrain.monkey_oldworld_TPM.gii
A  templates_animals_surfaces/lc.central.Template_chimpanzee_T1_GS.gii
A  templates_animals_surfaces/lh.central.Template_chimpanzee_T1_GS.gii
A  templates_animals_surfaces/mesh.central.Template_chimpanzee_T1_GS.gii
A  templates_animals_surfaces/rc.central.Template_chimpanzee_T1_GS.gii
A  templates_animals_surfaces/rh.central.Template_chimpanzee_T1_GS.gii
A  templates_surfaces/bh.headbrain.TPM.gii
A  templates_surfaces/cb.central.Template_T1.gii
A  templates_surfaces/cb.central.freesurfer.gii
A  templates_surfaces/cb.sphere.freesurfer.gii
A  templates_surfaces/lh.central.Template_T1.gii
A  templates_surfaces/lh.central.freesurfer.gii
A  templates_surfaces/lh.inflated.freesurfer.gii
A  templates_surfaces/lh.mc.freesurfer.gii
A  templates_surfaces/lh.patch.freesurfer.gii
A  templates_surfaces/lh.sphere.freesurfer.gii
A  templates_surfaces/lh.sqrtsulc.freesurfer.gii
A  templates_surfaces/mesh.central.Template_T1.gii
A  templates_surfaces/mesh.central.freesurfer.gii
A  templates_surfaces/mesh.inflated.freesurfer.gii
A  templates_surfaces/rh.central.Template_T1.gii
A  templates_surfaces/rh.central.freesurfer.gii
A  templates_surfaces/rh.inflated.freesurfer.gii
A  templates_surfaces/rh.mc.freesurfer.gii
A  templates_surfaces/rh.patch.freesurfer.gii
A  templates_surfaces/rh.sphere.freesurfer.gii
A  templates_surfaces/rh.sqrtsulc.freesurfer.gii
A  templates_surfaces_32k/lh.central.Template_T1.gii
A  templates_surfaces_32k/lh.central.freesurfer.gii
A  templates_surfaces_32k/lh.inflated.freesurfer.gii
A  templates_surfaces_32k/lh.mc.freesurfer.gii
A  templates_surfaces_32k/lh.patch.freesurfer.gii
A  templates_surfaces_32k/lh.sphere.freesurfer.gii
A  templates_surfaces_32k/lh.sqrtsulc.freesurfer.gii
A  templates_surfaces_32k/mesh.central.Template_T1.gii
A  templates_surfaces_32k/mesh.central.freesurfer.gii
A  templates_surfaces_32k/mesh.inflated.freesurfer.gii
A  templates_surfaces_32k/rh.central.Template_T1.gii
A  templates_surfaces_32k/rh.central.freesurfer.gii
A  templates_surfaces_32k/rh.inflated.freesurfer.gii
A  templates_surfaces_32k/rh.mc.freesurfer.gii
A  templates_surfaces_32k/rh.patch.freesurfer.gii
A  templates_surfaces_32k/rh.sphere.freesurfer.gii
A  templates_surfaces_32k/rh.sqrtsulc.freesurfer.gii
 M templates_volumes/hammers.txt

(1) Removed pdf/doc*-files from git.
(2) Added *.gii files again

------------------------------------------------------------------------
r2008 | gaser | 2022-07-04 22:12:34

Changed paths:
 M Amap.c
 M Bayes.c
 M BayesMex.c
D  CAT12-Manual-Word-Old.docx
D  CAT12-Manual.pdf
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
D  OverlayCAT12_cg.docx
 M Pve.c
D  "Sicherungskopie von CAT12-Manual.doc"
D  "Sicherungskopie von CAT12-Manual.docx"
D  VBM12-Manual_Japanese.doc
D  VBM12-Manual_Japanese.pdf
D  VBM8-flowchart.doc
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
 M cat_ornlm.c
 M cat_plot_circular.m
 M cat_sanlm.c
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
 M cat_vol_ROIval.c
 M cat_vol_downcut.c
 M cat_vol_eidist.c
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
 M cat_vol_gradient3.c
 M cat_vol_laplace3.c
 M cat_vol_laplace3R.c
 M cat_vol_localstat.c
 M cat_vol_median3.c
 M cat_vol_median3c.c
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
 M cat_vol_pbtp2.c
 M cat_vol_simgrow.c
 M cat_vol_smooth3X.m
 M check_pipeline_ROIs.m
 M genus0.c
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
 M templates_MNI152NLin2009cAsym/hammers.txt
 M templates_volumes/hammers.txt

(1) Removed pdf/doc*-files from git.
(2) Added *.gii files again

------------------------------------------------------------------------
r2007 | gaser | 2022-07-04 22:03:52

Changed paths:
 M Amap.c
 M Bayes.c
 M BayesMex.c
A  CAT12-Manual-Word-Old.docx
A  CAT12-Manual.pdf
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
A  OverlayCAT12_cg.docx
 M Pve.c
A  "Sicherungskopie von CAT12-Manual.doc"
A  "Sicherungskopie von CAT12-Manual.docx"
A  VBM12-Manual_Japanese.doc
A  VBM12-Manual_Japanese.pdf
A  VBM8-flowchart.doc
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
 M cat_ornlm.c
 M cat_plot_circular.m
 M cat_sanlm.c
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
 M cat_vol_ROIval.c
 M cat_vol_downcut.c
 M cat_vol_eidist.c
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
 M cat_vol_gradient3.c
 M cat_vol_laplace3.c
 M cat_vol_laplace3R.c
 M cat_vol_localstat.c
 M cat_vol_median3.c
 M cat_vol_median3c.c
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
 M cat_vol_pbtp2.c
 M cat_vol_simgrow.c
 M cat_vol_smooth3X.m
 M check_pipeline_ROIs.m
 M genus0.c
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
 M templates_MNI152NLin2009cAsym/hammers.txt
 M templates_volumes/hammers.txt

Added pdf/doc*-files again
------------------------------------------------------------------------
r2006 | gaser | 2022-07-04 22:01:20

Changed paths:
 M Amap.c
 M Bayes.c
 M BayesMex.c
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
A  KmeansMex.mexmaci64
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
 M Pve.c
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
A  cat_amap.mexa64
A  cat_amap.mexmaci64
A  cat_amap.mexw64
A  cat_amap_new.mexmaci64
 M cat_ornlm.c
A  cat_ornlm.mexa64
A  cat_ornlm.mexmaci
A  cat_ornlm.mexmaci64
A  cat_ornlm.mexw64
 M cat_plot_circular.m
 M cat_sanlm.c
A  cat_sanlm.mexa64
A  cat_sanlm.mexmaci64
A  cat_sanlm.mexw64
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
A  cat_vbdist.mexa64
A  cat_vbdist.mexmaci64
A  cat_vbdist.mexw64
 M cat_vol_ROIval.c
A  cat_vol_ROIval.mexmaci64
 M cat_vol_downcut.c
A  cat_vol_downcut.mexa64
A  cat_vol_downcut.mexmaci64
A  cat_vol_downcut.mexw64
 M cat_vol_eidist.c
A  cat_vol_eidist.mexa64
A  cat_vol_eidist.mexmaci64
A  cat_vol_eidist.mexw64
A  cat_vol_eikonal3.mexa64
A  cat_vol_eikonal3.mexmaci64
A  cat_vol_eikonal3.mexw64
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
A  cat_vol_genus0.mexa64
A  cat_vol_genus0.mexmaci64
A  cat_vol_genus0.mexw64
 M cat_vol_gradient3.c
A  cat_vol_gradient3.mexa64
A  cat_vol_gradient3.mexmaci64
A  cat_vol_gradient3.mexw64
A  cat_vol_interp3f.mexa64
A  cat_vol_interp3f.mexmaci64
A  cat_vol_interp3f.mexw64
 M cat_vol_laplace3.c
A  cat_vol_laplace3.mexa64
A  cat_vol_laplace3.mexmaci64
A  cat_vol_laplace3.mexw64
 M cat_vol_laplace3R.c
A  cat_vol_laplace3R.mexa64
A  cat_vol_laplace3R.mexmaci64
A  cat_vol_laplace3R.mexw64
 M cat_vol_localstat.c
A  cat_vol_localstat.mexa64
A  cat_vol_localstat.mexmaci64
A  cat_vol_localstat.mexw64
 M cat_vol_median3.c
A  cat_vol_median3.mexa64
A  cat_vol_median3.mexmaci64
A  cat_vol_median3.mexw64
 M cat_vol_median3c.c
A  cat_vol_median3c.mexa64
A  cat_vol_median3c.mexmaci64
A  cat_vol_median3c.mexw64
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
A  cat_vol_pbtp.mexa64
A  cat_vol_pbtp.mexmaci64
A  cat_vol_pbtp.mexw64
 M cat_vol_pbtp2.c
A  cat_vol_pbtp2.mexa64
A  cat_vol_pbtp2.mexmaci64
A  cat_vol_pbtp2.mexw64
A  cat_vol_pbtv.mexmaci64
 M cat_vol_simgrow.c
A  cat_vol_simgrow.mexa64
A  cat_vol_simgrow.mexmaci64
A  cat_vol_simgrow.mexw64
 M cat_vol_smooth3X.m
 M check_pipeline_ROIs.m
 M genus0.c
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
A  spm_diffeo_old.mexa64
A  spm_diffeo_old.mexmaci64
A  spm_diffeo_old.mexw64
 M templates_MNI152NLin2009cAsym/hammers.txt
 M templates_volumes/hammers.txt

Added mex-files again
------------------------------------------------------------------------
r2006 | gaser | 2022-07-04 22:00:24

Changed paths:
 M Amap.c
 M Bayes.c
 M BayesMex.c
 M CHANGES.txt
 M Contents.m
 M Kmeans.c
 M KmeansMex.c
 M MBeautify.m
 M MBeautify.txt
 M MFormatter.m
 M Makefile
 M MrfPrior.c
 M Pve.c
 M WarpPriors.c
 M atlases_surfaces/lh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces/rh.aparc_DK40.freesurfer.annot
 M atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
 M atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
 M cat_amap.c
 M cat_ornlm.c
 M cat_plot_circular.m
 M cat_sanlm.c
 M cat_stat_factorial_design.m
 M cat_stat_histth.m
 M cat_stat_kmeans.m
 M cat_surf_coregvol2surf.m
 M cat_vbdist.c
 M cat_vol_ROIval.c
 M cat_vol_downcut.c
 M cat_vol_eidist.c
 M cat_vol_findfiles.m
 M cat_vol_genus0.c
 M cat_vol_gradient3.c
 M cat_vol_laplace3.c
 M cat_vol_laplace3R.c
 M cat_vol_localstat.c
 M cat_vol_median3.c
 M cat_vol_median3c.c
 M cat_vol_nonlin_coreg.m
 M cat_vol_pbt.m
 M cat_vol_pbtp.c
 M cat_vol_pbtp.cpp
 M cat_vol_pbtp2.c
 M cat_vol_simgrow.c
 M cat_vol_smooth3X.m
 M check_pipeline_ROIs.m
 M genus0.c
 M html/cat.html
 M internal/cat_vol_cMRegularizarNLM3D.c
 M internal/cat_vol_cMRegularizarNLM3Dw.c
 M internal/cat_vol_gbdist.m
 M optimizer3d.c
 M ornlm_float.c
 M sanlm_float.c
 M spm_diffeo_old.c
 M templates_MNI152NLin2009cAsym/hammers.txt
 M templates_volumes/hammers.txt

Added mex-files again
------------------------------------------------------------------------
r2004 | gaser | 2022-07-04 17:56:51

Changed paths:
 M CHANGES.txt
 M git_ci_log
D  svn_ci_log

Removed svn_ci_log
------------------------------------------------------------------------
r2003 | gaser | 2022-07-04 17:43:35

Changed paths:
 M CHANGES.txt
 M git_ci_log

Add git_ci_log

------------------------------------------------------------------------
r2002 | gaser | 2022-07-04 17:40:44

Changed paths:
 M CHANGES.txt
MM git_ci_log

Replaced svn commands in Makefile by git commands

------------------------------------------------------------------------
r2001 | dahnke | 2022-06-17 22:39:58

Changed paths:
M       CHANGES.txt
M       cat_io_xml.m
M       cat_run_newcatch.m
M       cat_vol_qa.m

(1) Fixed:  Corrected bug in cat_io_xml that causes problems in cat_surf_surf2roi.
(2) Fixed:  Corrected bug in cat_vol_qa (smoothing).
(3) Fixed:  Corrected bug in cat_run_newcatch (missing variable).

------------------------------------------------------------------------
r2000 | gaser | 2022-06-17 14:56:48 +0200 (Fri, 17 Jun 2022) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       html/cat.html
M       html/cat.txt
M       html/cat_references.html

(1) Changed: Updated CAT12 references.

------------------------------------------------------------------------
r1999 | gaser | 2022-06-17 14:38:19 +0200 (Fri, 17 Jun 2022) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m

(1) Changed: Adapted call of spm_cfg_imcalc to newer functionality in SPM12
             in cat_conf_tools.m.

------------------------------------------------------------------------
r1998 | dahnke | 2022-06-17 11:57:40 +0200 (Fri, 17 Jun 2022) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_marks.m
M       cat_vol_headtrimming.m
M       cat_vol_qa.m
M       cat_vol_resize.m

(1) Fixed:     Light changes of the QC in cat_stat_marks and cat_vol_qa.
							 Adaptions for the edge-to-contrast-ratio (ECR) resolution measure
               res_ECR (previously named res_grad). Further added the structural
               image quality rating (SIQR) as successor of IQR that also include
               ECR. Replace old tissue peak estimation with cat_stat_nanmean by
               cat_stat_kmeans that should be more reliable (currently flagged
               for further tests).
(2) Fixed:     Tiny corrections in cat_vol_resize.
(3) Fixed:     Corrected bug in cat_vol_headtrimming with some atlas datasets.


------------------------------------------------------------------------
r1997 | gaser | 2022-06-16 11:17:25 +0200 (Thu, 16 Jun 2022) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_plot_boxplot.m
M       cat_plot_histogram.m
MM      cat_plot_scatter.m

(1) Changed: Added option to add jitter to categorical variables in
             cat_plot_scatter.m.
(2) Changed: Added more functionality to handle data arrays in
             cat_plot_histogram.m.
(3) Changed: Added option to add jittered data points with probability density
             as shape (similar to beeswwarm plot).


------------------------------------------------------------------------
r1996 | gaser | 2022-06-08 17:50:23 +0200 (Wed, 08 Jun 2022) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_plot_histogram.m
M       cat_plot_scatter.m
M       cat_vol_qa.m

(1) Changed: Added new flags to cat_plot_scatter.m.
(2) Fixed:   Corrected order of labels in cat_plot_histogram.m.
(3) Fixed:   Added missing paramter 'red' to cat_vol_qa.m.


------------------------------------------------------------------------
r1995 | gaser | 2022-05-24 17:22:04 +0200 (Tue, 24 May 2022) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_plot_histogram.m
A       cat_plot_scatter.m

(1) Added:   New function cat_plot_scatter to draw scatter plots coloured by
             density and to fit polynomial curves and add confidence interval.
(2) Changed: Replaced old 2d histogram function by scatter plot coloured by
             density using cat_plot_scatter.m.


------------------------------------------------------------------------
r1994 | gaser | 2022-05-23 16:57:46 +0200 (Mon, 23 May 2022) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_long_main.m
M       cat_surf_results.m
M       cat_vol_img2mip.m

(1) Changed: Added colorbar to single MIP in cat_vol_img2mip.m.
(2) Fixed:   Multiple volume files were not correctly recognized in
             cat_surf_results.m.
(3) Fixed:   Dartel export images of average image were always removed even
             if the Dartel save option was used.


------------------------------------------------------------------------
r1993 | gaser | 2022-05-19 11:23:00 +0200 (Thu, 19 May 2022) | 25 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_io_checkinopt.m
M       cat_stat_TIV.m
M       cat_surf_calc.m
M       cat_surf_results.m
M       cat_vol_img2mip.m
M       html/cat.html
M       html/cat_methods_SBM.html
M       html/cat_starting.html
M       standalone/cat_standalone.sh

(1) Changed: Extended cat_vol_img2mip.m to allow structure as input with many
             additional options such as colormap, range, func to mirror a bit
             the parameters of cat_vol_slice_overlay.m.
(2) Changed: Added visualization of MIP for volume data in cat_surf_results.m.
(3) Changed: Changed volume-to-surface mapping to equi-volume model as default
             and moved equi-distamce model to developer mode.
(4) Fixed:   Corrected handling of additional arguments in cat_standalone.sh.
(5) Fixed:   Corrected estimation of filename and path in cat_stat_TIV.m.
(6) Fixed:   Corrected handling of surfaces without faces/vertices in
             cat_surf_calc.m

------------------------------------------------------------------------
r1992 | dahnke | 2022-05-13 10:05:20 +0200 (Fri, 13 May 2022) | 22 lines

Changed paths:
M       CHANGES.txt
M       cat_main_reportfig.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_stat_marks.m
M       cat_vol_pbt.m
M       cat_vol_qa.m

(1) Fixed:     Corrected filter setting in cat_long_main.
(2) Fixed:     Switch GM and WM volume in cat_main_reportfig.
               Modified plot scales and added TSA and thickness.
(3) Changed:   Changed SPM preprocessing iteration parameter in
               cat_run_job[1639] to force higher minimum iteration
               number only in longitudinal processing.
(4) Changed:   Updated unused boundary box quality measure in
               cat_vol_qa and cat_stat_marks.
(5) Fixed:     Corrected typo in cat_vol_pbt.
(6) Fixed:     Set new IQR rating (under test) only for developers
               in cat_stat_marks.


------------------------------------------------------------------------
r1991 | gaser | 2022-05-11 16:16:31 +0200 (Wed, 11 May 2022) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_surf_results.m
M       cat_vol_slice_overlay.m

(1) Changed: Extended cat_surf_results.m to show interactive slice overlay if
             volume data are used as result.
(2) Changed: Added pos-flag to cat_vol_slice_overlay.m to define location of
             overlay window.
(3) Fixed:   Corrected some typos in cat_conf_tools.m

------------------------------------------------------------------------
r1990 | gaser | 2022-05-06 15:36:53 +0200 (Fri, 06 May 2022) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_TIV.m

(1) Fixed:   Corrected bug in cat_stat_TIV.m if no filedata field was found in
             xml-file.


------------------------------------------------------------------------
r1989 | gaser | 2022-05-06 11:16:31 +0200 (Fri, 06 May 2022) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_io_data2mat.m
M       standalone/cat_standalone.sh
M       templates_MNI152NLin2009cAsym/cobra.txt

(1) Changed: Updated help text and references for atlases used in CAT12.
(2) Changed: Updated some general help text.
(3) Fixed:   Corrected bug for saving surface data as mat file in
             cat_io_data2mat.m.


------------------------------------------------------------------------
r1988 | gaser | 2022-05-02 12:30:43 +0200 (Mon, 02 May 2022) | 27 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_stat_TIV.m
M       cat_vol_qa.m
M       html/cat.html
M       html/cat_licences.html
M       spm_cat12.m
M       standalone/cat_standalone.sh
M       standalone/cat_standalone_get_TIV.m

(1) Changed: Extended cat_stat_TIV to also optionally add filename and folder
             to 1st column of output file.
(2) Changed: Extended cat_standalone.sh to allow 3rd parameter.
(3) Changed: Added 3rd parameter to cat_standalone_get_TIV.m to to also
             optionally add filename and folder to output file.
(4) Changed: Updated references in cat_licences.html.
(5) Changed: Enabled extraction of surface ratio as new folding measure in
             cat_conf_stools.m.
(6) Changed: Updated GUI names for standard CAT12 mode in cat12.m.
(7) Fixed:   Corrected typo in spm_cat12.m that called not existing command.
(8) Fixed:   Added check for variable Pp0 to cat_vol_qa.m.


------------------------------------------------------------------------
r1987 | gaser | 2022-04-25 14:28:37 +0200 (Mon, 25 Apr 2022) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_system.m
M       spm_cat12.m

(1) Changed: Added check to spm_cat12.m to check whether mex-files on MAC OS
             are blocked.

------------------------------------------------------------------------
r1986 | gaser | 2022-04-25 13:45:39 +0200 (Mon, 25 Apr 2022) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_analyze_ROIs.m
 M      html/cat_shell.html

(1) Changed: Added check to cat_stat_analyze_ROI.m to indicate ROI values that
             have low relative values and should be care with caution.

------------------------------------------------------------------------
r1985 | gaser | 2022-04-25 09:18:54 +0200 (Mon, 25 Apr 2022) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_parallelize.m
M       cat_plot_histogram.m
M       cat_vol_img2mip.m
MM      cat_vol_sanlm2.m
M       standalone/cat_standalone.sh
MM      standalone/cat_standalone_get_TIV.m

(1) Changed: Prevent heavy use of nano editor in cat_parallelize.m in
             headless mode without GUI.
(2) Fixed:   Corrected bug in cat_vol_img2mip.m that was caused if one view
             was empty.


------------------------------------------------------------------------
r1984 | gaser | 2022-04-19 09:59:02 +0200 (Tue, 19 Apr 2022) | 49 lines

Changed paths:
M       CHANGES.txt
M       cat_amap.mex
M       cat_conf_factorial.m
M       cat_io_xml.m
M       cat_long_main.m
M       cat_ornlm.mex
M       cat_parallelize.m
M       cat_run.m
M       cat_sanlm.mex
M       cat_stat_TIV.m
M       cat_surf_results.m
M       cat_vbdist.mex
M       cat_vol_downcut.mex
M       cat_vol_eidist.mex
M       cat_vol_genus0.mex
M       cat_vol_gradient3.mex
M       cat_vol_interp3f.mex
M       cat_vol_laplace3.mex
M       cat_vol_laplace3R.mex
M       cat_vol_localstat.mex
M       cat_vol_median3.mex
M       cat_vol_median3c.mex
M       cat_vol_pbtp.mex
M       cat_vol_simgrow.mex
M       html/cat.txt
M       html/cat_licences.html
A       html/cat_shell.html
M       internal/cat_vol_cMRegularizarNLM3D.mex
M       standalone/cat_standalone.sh

(1) Changed: Extended cat_standalone.sh to also allow calling any SPM12/CAT12
             batch in standard Matlab.
(2) Changed: Extended cat_surf_results to set title of colorbar and to
             automatically estimate path and filename for saving.
(3) Changed: Option for independence in cat_conf_factorial.m is now visible.
(4) Fixed:   Corrected bug in cat_stat_TIV.m where filename could not be
             estimated using xml-structure.
(5) Fixed:   Added check for defects file in cat_surf_createCS2.m that is
             sometimes missing for some unknown reason.
(6) Fixed:   Corrected bug cat_run.m where octave options were not correctly
             considered for spatial registration.
(7) Fixed:   Deleting temporary files in cat_long_main.m was not working
             for some options of prepavg.
(8) Fixed:   Some octave options in cat_io_xml.m for checking java were not
             working.
(9) Fixed:   Use of edit-command not only worked for all systems in
             cat_parallelize.m.

------------------------------------------------------------------------
r1983 | dahnke | 2022-04-14 16:18:41 +0200 (Thu, 14 Apr 2022) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_long_main.m

(1) Fixed:     Corrected filter setting in cat_long_main.

------------------------------------------------------------------------
r1982 | dahnke | 2022-04-12 13:09:13 +0200 (Tue, 12 Apr 2022) | 27 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_long_report.m
M       cat_main_reportfig.m
M       cat_stat_marks.m
M       cat_vol_groupwise_ls.m
M       cat_vol_qa.m
M       cat_vol_resize.m
M       cat_vol_sanlm.m
A       cat_vol_sanlm2.m

(1) Fixed:     Corrected some bugs in cat_vol_qa when it is called as batch.
               Corrected bias-correction WM threshold in case of batch input.
(2) Fixed:     Corrected dependencies of QC batch in cat_conf_tools.
(3) New:       Added res_grad measure scaling in cat_
(4) Fixed:     Corrections in cat_long_report in case of missing xml data.
               Added missing default settings in cat_main_reportfig.
(5) New:       Renamed cat_vol_sanlm to cat_vol_sanlm2 and create a new batch
               in cat_conf_tools.
               Added low-resolution filter test to avoid overfiltering, and
               new resolution measure and further outputs.
(6) Reset:     Revert cat_vol_sanlm to revision 1936.
(7) Changed:   Small adaptions in cat_vol_groupwise_ls to control the
               average resolution.


------------------------------------------------------------------------
r1981 | gaser | 2022-04-04 09:23:37 +0200 (Mon, 04 Apr 2022) | 30 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_surf_createCS2.m
M       cat_surf_surf2roi.m
M       html/cat.html
M       standalone/cat_standalone.sh
M       standalone/cat_standalone_deface.m
M       standalone/cat_standalone_dicom2nii.m
M       standalone/cat_standalone_get_ROI_values.m
A       standalone/cat_standalone_get_TIV.m
M       standalone/cat_standalone_get_quality.m
M       standalone/cat_standalone_resample.m
M       standalone/cat_standalone_segment.m
M       standalone/cat_standalone_segment_enigma.m
M       standalone/cat_standalone_segment_long.m
M       standalone/cat_standalone_simple.m
M       standalone/cat_standalone_smooth.m
M       standalone/cat_standalone_tfce.m

(1) Changed: Updated help text for standalone tools.
(2) Changed: Added standalone tool for estimating TIV.
(3) Changed: Replaced matlab.lang.makeUniqueStrings by older genvarname to
             ensure compatibility with older Matlab versions in cat12.m.
(4) Fixed:   Corrected handling different atlases in cat_surf_surf2roi.m.
(5) Fixed:   Added check for defects file in cat_surf_createCS2.m that is
             sometimes missing for some unknown reason.


------------------------------------------------------------------------
r1980 | gaser | 2022-03-30 16:40:08 +0200 (Wed, 30 Mar 2022) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_roi_fun.m
M       cat_run_job.m
M       html/cat.html

(1) Changed: Removed catROI(2)_ from output filename for writing csv files
             to summarize ROI measures.
(2) Fixed:   Removed comment in cat_run_job.m that caused trouble for compiling.


------------------------------------------------------------------------
r1979 | gaser | 2022-03-30 16:12:01 +0200 (Wed, 30 Mar 2022) | 20 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_conf_stools.m
M       cat_stat_analyze_ROIs.m
M       cat_vol_sanlm.m
M       html/cat.html
M       html/cat_versions.html
M       standalone/cat_standalone.sh
M       standalone/cat_standalone_segment_long.m

(1) Changed: Updated standalone tools and help text.
(2) Changed: Hide option for merging hemipsheres in "Resample & Smooth".
(3) Fixed:   Corrected handling of additional arguments in cat_standalone.sh.
(4) Fixed:   Corrected error in Holm-Bonferroni correction in
             cat_stat_analyze_ROIs.m
(5) Fixed:   Corrected handling of floating values in expert mode in
             cat_vol_sanlm.m.

------------------------------------------------------------------------
r1978 | gaser | 2022-03-25 22:51:43 +0100 (Fri, 25 Mar 2022) | 17 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_stat_check_cov.m
M       cat_surf_results.m
M       html/cat.html
M       html/cat_versions.html
M       spm_cat12.m

(1) Changed: Updated manual and version information.
(2) Fixed:   Removed bug in cat_stat_check_cov.m if no text-interpreter could
             be found for data cursor.
(3) Fixed:   Corrected handling of surface data in cat_surf_results.m where
             no texture data are available.

------------------------------------------------------------------------
r1977 | dahnke | 2022-03-22 14:24:14 +0100 (Tue, 22 Mar 2022) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_long_report.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m

(1) Fixed:     Corrected bugs in long pipeline in case of BIDS data.
(2) Fixed:     Corrected prior setup in longitudinal timepoints in
               cat_main_updateSPM(1639) in case of BIDS data.

------------------------------------------------------------------------
r1976 | gaser | 2022-03-21 13:38:34 +0100 (Mon, 21 Mar 2022) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_cat.sh
M       cat_batch_long.m
M       cat_batch_long.sh
M       cat_conf_output.m
M       cat_defaults.m
M       cat_main_reportfig.m
M       cat_plot_glassbrain.m
M       standalone/cat_parallelize.sh
M       standalone/cat_standalone.sh

(1) Changed: Updated help text in several functions.
(2) Changed: Added flag for using BIDS to cat_defaults.m.
(3) Changed: Added flag for using BIDS to shell-scripts.

------------------------------------------------------------------------
r1975 | dahnke | 2022-03-21 09:00:58 +0100 (Mon, 21 Mar 2022) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_long.m
M       cat_long_main.m
M       cat_long_report.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_surf_display.m
M       cat_surf_info.m

(1) Fixed:     Limited use of the longitudinal development model to developer
               (cat_conf_long)
(2) New:       Extended todo list and comments in cat_long_main.
(3) New:       Extended cat_long_report (cat_main_reportstr, cat_main_reportfig)
               by longitudinal parameters.
(4) Fixed:     Tried to correct use of internal subject-specific surface data in
               case of resampled surface in cat_surf_display and cat_surf_info.


------------------------------------------------------------------------
r1974 | dahnke | 2022-03-16 16:14:54 +0100 (Wed, 16 Mar 2022) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_long_multi_run.m

(1) Fixed:     Corrected bug with jobs variable in cat_long_multi_run.

------------------------------------------------------------------------
r1973 | dahnke | 2022-03-16 15:32:01 +0100 (Wed, 16 Mar 2022) | 20 lines

Changed paths:
M       CHANGES.txt
M       cat_io_volctype.m
M       cat_long_main.m
M       cat_long_multi_run.m
M       cat_long_report.m
M       cat_main_reportfig.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_surf_create_TPM_hull_surface.m

(1) Fixed:     Corrected trimming and sanlm batch setup in cat_long_main.
(2) Fixed:     Corrected skull-stripping bug in cat_main_updateSPM again.
(3) Fixed:     Corrected display bugs in cat_io_volctype.
(4) Changed:   Improved differentiation of TPM cases in
               cat_surf_create_TPM_hull_surface.
(5) New:       Added creation of catlong XML file to save longitudinal
               parameters in cat_long_multi_run and cat_long_report.


------------------------------------------------------------------------
r1972 | dahnke | 2022-03-16 11:32:57 +0100 (Wed, 16 Mar 2022) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_vol_headtrimming.m

(1) Fixed:     Corrected bugs in cat_vol_headtrimming in case of multiple inputs
               per subject. Removed average parameter (also in cat_conf_tools).
(2) Fixed:     Improved handling of background detection in case of skull-
               stripped images in cat_run_job(1639).


------------------------------------------------------------------------
r1971 | gaser | 2022-03-08 13:43:17 +0100 (Tue, 08 Mar 2022) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_check_cov.m
M       check_pipeline_homogeneity.m
M       html/cat.html

(1) Changed: Updated check_pipeline_homogeneity.m to ignore older versions.
(2) Fixed:   Corrected indexing of data_vol field in cat_stat_check_cov.m.

------------------------------------------------------------------------
r1970 | gaser | 2022-03-08 11:01:28 +0100 (Tue, 08 Mar 2022) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_confplot_spm.m
M       cat_vol_avg.m
M       cat_vol_slice_overlay.m

(1) Changed: Updated help text for cat_vol_slice_overlay.m.
(2) Changed: Added interactive call to cat_vol_avg.m.
(3) Changed: Changed default boxplot to density plot in cat_stat_confplot_spm.m.

------------------------------------------------------------------------
r1969 | dahnke | 2022-03-07 21:58:24 +0100 (Mon, 07 Mar 2022) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_io_volctype.m
M       cat_vol_headtrimming.m

(1) Fixed:   Extended intensity scaling setup of trimming batch to support
             unscaled cases and extended reports and warnings. E.g. in case of
             severe cut-offs by selecting inoptimal data types or scaling range.

------------------------------------------------------------------------
r1968 | dahnke | 2022-03-06 21:21:34 +0100 (Sun, 06 Mar 2022) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_io_volctype.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_stat_histth.m
M       cat_surf_createCS2.m
M       cat_vol_headtrimming.m
M       cat_vol_sanlm.m

(1) Fixed:   Reversed unwanted submission of cat_surf_createCS in previous version.
(2) Fixed:   Corrected problems in cat_io_volctype with small changes in
             cat_stat_histth and cat_io_headtrimming.
(3) Fixed:   Added missed variable in cat_vol_sanlm.
(4) Changed: Modified handling of detected skull in case of inactive
             skull-stripping in cat_run_job(1639).


------------------------------------------------------------------------
r1967 | dahnke | 2022-03-06 21:05:57 +0100 (Sun, 06 Mar 2022) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_vol_sanlm.m

(1) Changed:  Added new filter setups to filter images that should be averaged.
              Added further denoising measures also for lower resolution.
(2) Fixed:    Corrected data type bug in cat_conf_tools.


------------------------------------------------------------------------
r1966 | dahnke | 2022-03-05 15:26:08 +0100 (Sat, 05 Mar 2022) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_sanlm.m

(1) Fixed:   Corrected bug in cat_vol_sanlm due to missing datafield.

------------------------------------------------------------------------
r1965 | dahnke | 2022-03-05 13:44:38 +0100 (Sat, 05 Mar 2022) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_vol_sanlm.m

(1) Fixed:   Corrected settings of parameters in cat_vol_sanlm.

------------------------------------------------------------------------
r1964 | dahnke | 2022-03-03 14:01:45 +0100 (Thu, 03 Mar 2022) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_run_job1639.m
M       cat_surf_createCS2.m
M       cat_vol_groupwise_ls.m

(1) Fixed:   Corrected bug in the estimation of isotropic resolutions in the
             longitidunal average creation cat_vol_groupwise_ls.

------------------------------------------------------------------------
r1963 | dahnke | 2022-03-03 10:51:09 +0100 (Thu, 03 Mar 2022) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_info.m
M       cat_surf_render2.m

(1) Fixed:   Corrected bugs in displaying surface textures.

------------------------------------------------------------------------
r1962 | gaser | 2022-03-02 14:49:28 +0100 (Wed, 02 Mar 2022) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_sanlm.m

Fixed: For skull-stripped data noise while using sanlm-filter was added even
       in zero-valued areas.

------------------------------------------------------------------------
r1961 | gaser | 2022-03-02 14:11:59 +0100 (Wed, 02 Mar 2022) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_vol_sanlm.m
M       html/cat.html

Fixed: For skull-stripped data noise while using sanlm-filter was added even
       in zero-valued areas.

------------------------------------------------------------------------
r1960 | dahnke | 2022-03-01 17:31:23 +0100 (Tue, 01 Mar 2022) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_long_main.m
M       cat_long_report.m

(1) Fixed:   Corrected bugs in cat_long_main and cat_long_report.

------------------------------------------------------------------------
r1959 | dahnke | 2022-03-01 15:22:21 +0100 (Tue, 01 Mar 2022) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_groupwise_ls.m
M       cat_vol_series_align.m

(1) New:      Added parameter to force isotropic resolution in longitudinal
              average estimation in cat_vol_groupwise_ls controlled in
              cat_vol_series_align. Currently, the optimized version is active
              that will optimize the resolution if the input resolution is not
              isotropic.


------------------------------------------------------------------------
r1958 | dahnke | 2022-02-28 22:42:18 +0100 (Mon, 28 Feb 2022) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_long.m
M       cat_long_main.m

(1) New:      Added new longitudinal development model (0) that focuses on the
              cross-sectional pipeline. The model includes use of an average
              based TPM creation to improve the longitudinal processing.
              Major changes in cat_long_main and cat_conf_long.


------------------------------------------------------------------------
r1957 | dahnke | 2022-02-28 21:10:19 +0100 (Mon, 28 Feb 2022) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_io_file_move.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_surf_fun.m

(1) New:      Added handling of copyto the same directory in cat_io_file_move.
(2) Fixed:    Corrected test for TPM in cat_run_job(1639).
(3) Fixed:    Corrected small bug in cat_main_updateSPM(1639) for longitudinal
              skull-stripping with prior.
(4) New:      Added tnear function in cat_surf_fun.


------------------------------------------------------------------------
r1956 | dahnke | 2022-02-28 20:48:23 +0100 (Mon, 28 Feb 2022) | 20 lines

Changed paths:
M       CHANGES.txt
M       cat_long_report.m
M       cat_main_reportcmd.m
M       cat_main_reportfig.m
M       cat_stat_check_cov.m
MM      cat_surf_flipvalues.m
M       cat_surf_info.m
MM      cat_surf_laterality_index.m
M       cat_surf_rename.m

(1) New:      Added internal resampling of cross-sectional input meshes in
              cat_long_report. No output of difference maps by default.
(2) Fixed:    Corrected tiny bugs in cat_main_reportcmd and cat_main_reportfig.
(3) Fixed:    Tiny correction in cat_stat_check_cov.
(4) Fixed:    Corrected problem of loading individual surface mesh rather than
              the FS average and incorrect setting of resampled32k suraces in
              cat_surf_info and cat_surf_rename.


------------------------------------------------------------------------
r1955 | dahnke | 2022-02-28 14:59:17 +0100 (Mon, 28 Feb 2022) | 22 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main1639.m
M       cat_main_write.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_run_newcatch.m
M       cat_stat_getCSVXMLfield.m
M       cat_vol_resize.m

(1) Fixed:    Added try-catch-block around ROI export in cat_main(1639).
(2) Fixed:    Correded bug in cat_main_write to handle atlas home directories in
              non-human cases.
(3) Fixed:    Corrected bug in cat_run in displaying processing errors of
              running parallel jobs.
(4) Fixed:    Corrected MRI directory bug in cat_run_newcatch.
(5) Fixed:    Path corrections in cat_stat_getCSVXMLfield.
(6) Fixed:    Corrected small data type bug in cat_vol_resize.


------------------------------------------------------------------------
r1954 | dahnke | 2022-02-28 12:04:43 +0100 (Mon, 28 Feb 2022) | 22 lines

Changed paths:
M       CHANGES.txt
M       cat_long_report.m
M       cat_main_reportfig.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_spm_preproc8.m

(1) Fixed:   Corrected longitudinal structural plot in cat_long_report and
             cat_main_reportfig.
(2) Changed: Extended SPM US stop criteria in cat_spm_preproc8 to avoid too
             early stops, i.e. after strong recent improvements. Added command
             line output of ll parameters for outer loops in developer mode.
             Added control variable in cat_run_job(1639) to switch between major
             settings. However, the differences between the even very low number
             and high number of iterations are relative small. Hence, I reduced
             the number of inner interactions and reset the increased amount of
             minimum outer iterations from 20 to 10 to speed up the process.
(3) Fixed:   Corrected bug where ll becomes nan in cat_spm_preproc8.



------------------------------------------------------------------------
r1953 | gaser | 2022-02-27 22:03:20 +0100 (Sun, 27 Feb 2022) | 8 lines

Changed paths:
M       CHANGES.txt
MM      cat_vol_img2mip.m
M       cat_vol_morph.m

Fixed: Corrected output of cat_vol_morph.m that was not correctly returned
       for multiple calls.

------------------------------------------------------------------------
r1952 | gaser | 2022-02-23 16:42:07 +0100 (Wed, 23 Feb 2022) | 15 lines

Changed paths:
M       CHANGES.txt
A       cat_surf_flipvalues.m
A       cat_surf_laterality_index.m
M       cat_surf_rename.m
M       cat_vol_morph.m

(1) Changed: Added wrapper to interactively call vat_vol_morph.m.
(2) Fixed:   Corrected handling of 32k-meshes in cat_surf_rename.m
(3) Added:   New function cat_surf_flipvalues to flip values in resampled
             32k-meshes.
(4) Added:   New function cat_surf_laterality_index to calculate laterality
             index in resampled 32k-meshes.


------------------------------------------------------------------------
r1951 | gaser | 2022-02-23 09:45:57 +0100 (Wed, 23 Feb 2022) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m
M       cat_surf_results.m
A       cat_vol_img2mip.m
 M      templates_MNI152NLin2009cAsym/suit.csv
 M      templates_MNI152NLin2009cAsym/suit.nii
MM      templates_MNI152NLin2009cAsym/suit.txt

(1) Changed: Updated help text in cat_surf_results.m
(2) Changed: Enabled eigenvariate and CVA function in cat_spm_results_ui.m.
(3) Fixed:   Added check that directory that is saved in SPM.mat really exists
             to cat_spm_results_ui.m.


------------------------------------------------------------------------
r1950 | gaser | 2022-02-21 21:10:37 +0100 (Mon, 21 Feb 2022) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_ROI.m
M       cat_conf_long.m
M       html/cat.html
M       templates_MNI152NLin2009cAsym/suit.csv
M       templates_MNI152NLin2009cAsym/suit.nii

(1) Changed: Changed default value for prepavg in longitudinal pipeline to 2.
(2) Changed: Updated default license for SUIT atlas.
(3) Fixed:   Corrected orientation of SUIT atlas  where x-voxel size was not
             negative (neurological orientation).


------------------------------------------------------------------------
r1949 | gaser | 2022-02-20 23:55:40 +0100 (Sun, 20 Feb 2022) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_ROI.m
M       cat_defaults.m
M       cat_run.m
M       cat_vol_avg.m
M       html/cat.html
M       html/cat_licences.html
M       html/cat_methods_RBM.html
A       templates_MNI152NLin2009cAsym/suit.csv
A       templates_MNI152NLin2009cAsym/suit.nii
A       templates_MNI152NLin2009cAsym/suit.txt

Changed: Added SUIT atlas of the human cerebellum.

------------------------------------------------------------------------
r1948 | dahnke | 2022-02-16 16:39:23 +0100 (Wed, 16 Feb 2022) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_io_volctype.m
M       cat_long_main.m
M       cat_main_updateSPM.m
M       cat_run_job1639.m
M       cat_vol_headtrimming.m

(1) Changed:  Small unfinished corrections to solve datatype bug
              in cat_io_volctype, cat_vol_headtripping.
(2) Fixed:    Corrected bug in cat_main_updateSPM.
(3) Changed:  Prototype for non-linear AVG for the developmental
              longitudinal model in cat_long_main.
(4) Changed:  Tiny modification of the cml output in cat_run_job1639.


------------------------------------------------------------------------
r1947 | dahnke | 2022-02-15 14:50:24 +0100 (Tue, 15 Feb 2022) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_long_main.m
M       cat_long_report.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_run_job1639.m
M       html/cat_methods_catlongreport.html

(1) Fixed:   Added development case to longitudinal report (unfinished).
(2) Fixed:   Corrected tiny bug in the setup of the development pipeline.
(3) Changed: Added development case to longitudinal help page (unfinished).
(4) Changed: Setup parameters to clear temporary report data.



------------------------------------------------------------------------
r1946 | dahnke | 2022-02-14 12:23:23 +0100 (Mon, 14 Feb 2022) | 30 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_long.m
M       cat_long_main.m
M       cat_main_amap.m
M       cat_main_amap1639.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_vol_groupwise_ls.m
M       cat_vol_series_align.m

(1) Fixed:   Updated setup of the initial segmentation setup of the AMAP
             to prevent errors in cat_main_amap.
(2) Fixed:   Corrected definition of the longitudinal brain mask in case
             of internally interpolated images that finally crashed the
             AMAP segmentation above (e.g., in NIH-NBD but not in ADNI).
(3) New:     Added longitudinal development model that is quite similar as
             the longitudinal aging model but uses a time point independent
             affine registration to adapt for brain/head growth.
             Changes in cat_conf_long (model setup), cat_long_main (affreg
             settings), cat_run_job[1639] (affreg handling).
(4) Fixed:   Corrected settings of the longitudinal deformation model to
             create the average (not used yet) in cat_long_main and in
             cat_vol_series_align. Further comments in cat_vol_groupwise_ls.
(5) Fixed:   Deactivated surface output if no prior surface but time point
             specific surfaces are used.


------------------------------------------------------------------------
r1945 | dahnke | 2022-02-07 22:40:22 +0100 (Mon, 07 Feb 2022) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_long_main.m

(1) New:     Corrected typos in cat_long_main.

------------------------------------------------------------------------
r1944 | dahnke | 2022-02-07 18:49:38 +0100 (Mon, 07 Feb 2022) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_long.m
M       cat_conf_tools.m
MM      cat_io_file_move.m
M       cat_long_biascorr.m
M       cat_long_main.m
M       cat_parallelize.m

(1) New:     Added detection of broken longitudinal batches in case
             of parallel processing in cat_parallelize.
(2) Fixed:   Added prepavg and avgLASWMHC parameters in cat_conf_long
             and cat_long_main for the further test in the developer mode.
(3) Fixed:   Corrected bugs in the renaming batch in cat_conf_tools.


------------------------------------------------------------------------
r1943 | dahnke | 2022-02-04 17:53:42 +0100 (Fri, 04 Feb 2022) | 22 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_long_main.m
M       cat_long_report.m
M       cat_main_reportfig.m
M       cat_main_updateSPM1639.m
M       cat_plot_glassbrain.m
M       cat_vol_groupwise_ls.m
M       cat_vol_set_com.m

(1) Fixed:   Further improvements of the CAT long report in
             cat_long_report and cat_main_reportfig.
(2) Fixed:   Create symmetric colormap image in cat_plot_glassbrain
             to allow simple scaling in cat_vol_reportfig.
(3) Fixed:   Corrected a bug in cat_main_upateSPM in case of low resolution
             data in the longitudinal preprocessing.
(4) Changed: Tiny corrections in cat_vol_set_com and cat_vol_groupwise_ls.




------------------------------------------------------------------------
r1942 | gaser | 2022-02-03 17:16:54 +0100 (Thu, 03 Feb 2022) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_long_main.m
M       cat_stat_check_cov.m
M       cat_vol_groupwise_ls.m
M       cat_vol_series_align.m

(1) Changed: Added support for setting origin using center-of-mass in
             longitudinal registration.
(2) Fixed:   Corrected axis scaling in cat_stat_check_cov.m for some cases.


------------------------------------------------------------------------
r1941 | dahnke | 2022-02-03 16:25:50 +0100 (Thu, 03 Feb 2022) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
A       cat_io_file_move.m
M       cat_long_biascorr.m
M       cat_long_main.m
M       cat_long_report.m
M       cat_main_reportfig.m

(1) Fixed:   Corrected directory bug in cat_long_main that moved all
             time points to the first directory.
(2) Changed: Replace first volume plot of a possible error map by save WM
             change plot and removed the WM plot batches in cat_long_main.
(3) New:     Added a copy of the SPM IO filename batch to rename filenames
             without changing the directory that is required to avoid the
             directory bug (see (1) ).


------------------------------------------------------------------------
r1940 | gaser | 2022-02-02 16:39:30 +0100 (Wed, 02 Feb 2022) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_long_report.m
M       cat_stat_check_cov.m

(1) Fixed: Added additional check for raw thickness data to cat_stat_check_cov.m.
           and added check for missing gap-field.
(2) Fixed: Changed wrong data field for cat_stat_check_cov in cat_long_report.m.


------------------------------------------------------------------------
r1939 | gaser | 2022-02-02 10:50:35 +0100 (Wed, 02 Feb 2022) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_long_main.m
M       cat_stat_check_cov.m

(1) Changed: Corrected data field in cat_stat_check_cov which is the same for
             volume as well as surface data.


------------------------------------------------------------------------
r1938 | dahnke | 2022-02-02 09:11:40 +0100 (Wed, 02 Feb 2022) | 34 lines

Changed paths:
M       CHANGES.txt
M       cat_long_biascorr.m
M       cat_long_main.m
MM      cat_long_report.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
MM      cat_plot_glassbrain.m
M       cat_run_job.m
M       cat_run_job1639.m
 M      html/cat_methods_catlongreport.html
MM      html/images/cat_long_report_plasticity-aging_ADNI011S0003.jpg
 M      html/images/cat_long_report_scannerdifferences_ADNI002S0559.jpg
 M      html/images/catlongreportj_mwp1r.jpg

(1) Fixed:   Corrected typos in plasticity-aging figure.
(2) Changed: Corrections in cat_long_biascorr to improve the longitudinal
             bias correction by replacing the median-based tissue threshold
             estimation by kmeans and further filtering terms to create a
             smoother bias-correction field.
             Also added a new further internal option to remove protocol-
             depending intensity changes by a simplified LAS approach.
             Although both elements work, recent tests did not show the
             hoped for improvements in the ADNI test data.
(3) Fixed:   Added further setting to detect XML files and improved handling
             of some fields in cat_long_report and cat_main_reportstr.
(4) Fixes:   Corrected many small display bugs in cat_main_reportfig.
(5) Tested:  Checked processing of longitudinal models.
(6) Fixed:   Corrected tiny bugs in cat_long_main.
(7) Fixed:   Corrected settings of resolution warnings in cat_run[1639].
(8) Fixed:   Corrected bug that avoid printing of the long report if only
             the aging model was used.


------------------------------------------------------------------------
r1937 | gaser | 2022-01-31 12:48:19 +0100 (Mon, 31 Jan 2022) | 37 lines

Changed paths:
M       CAT.maca64/CAT_3dVol2Surf
M       CAT.maca64/CAT_AddValuesToSurf
M       CAT.maca64/CAT_AverageSurfaces
M       CAT.maca64/CAT_BlurSurfHK
M       CAT.maca64/CAT_Central2Pial
M       CAT.maca64/CAT_DeformSurf
M       CAT.maca64/CAT_DumpCurv
M       CAT.maca64/CAT_DumpSurfArea
M       CAT.maca64/CAT_DumpSurfaceRatio
M       CAT.maca64/CAT_FixTopology
M       CAT.maca64/CAT_FractalDimension
M       CAT.maca64/CAT_Hausdorff
M       CAT.maca64/CAT_Isometize
M       CAT.maca64/CAT_MarkDefects
M       CAT.maca64/CAT_RefineMesh
M       CAT.maca64/CAT_ResampleSphericalSurf
M       CAT.maca64/CAT_ResampleSphericalSurfSPH
M       CAT.maca64/CAT_ResampleSurf
M       CAT.maca64/CAT_SelfIntersect
M       CAT.maca64/CAT_SeparatePolygon
M       CAT.maca64/CAT_SmoothConvexity
M       CAT.maca64/CAT_SulcusDepth
M       CAT.maca64/CAT_Surf2Sphere
M       CAT.maca64/CAT_Surf2Vol
M       CAT.maca64/CAT_SurfDistance
M       CAT.maca64/CAT_WarpSurf
M       CHANGES.txt
M       Makefile
M       cat_long_main.m
M       cp_binaries.sh

(1) Changed: Recompiled CAT-binaries for Apple ARM processors.
(2) Changed: Updated folder for binaries in Makefile and cp_binaries.
(3) Fixed:   Corrected expert-dependent parameters in cat_long_main.m.


------------------------------------------------------------------------
r1936 | dahnke | 2022-01-28 15:37:43 +0100 (Fri, 28 Jan 2022) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_long_report.m

(1) Fixed:   Corrected tiny bugs in cat_long_report.

------------------------------------------------------------------------
r1935 | dahnke | 2022-01-28 13:47:57 +0100 (Fri, 28 Jan 2022) | 54 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_long_main.m
A       cat_long_report.m
M       cat_main_reportcmd.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
A       cat_plot_glassbrain.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_run_job_APRGs.m
M       cat_stat_check_cov.m
M       cat_surf_createCS.m
M       cat_surf_display.m
M       cat_vol_groupwise_ls.m
M       cat_vol_headtrimming.m
M       cat_vol_qa.m
M       cat_vol_series_align.m
M       html/cat.html
M       html/cat_methods.html
M       html/cat_methods_LP.html
M       html/cat_methods_affreg.html
A       html/cat_methods_catlongreport.html
A       html/images/cat_long_report_plasticity-aging_ADNI011S0003.jpg
A       html/images/cat_long_report_scannerdifferences_ADNI002S0559.jpg
A       html/images/catlongreportj_mwp1r.jpg

(1) New:      Added first prototype of a longitudinal report to cat_conf_tools and
              cat_long_main. This also includes all updates in cat_main_reportfig,
              cat_main_reportstr and cat_plot_glassbrain. Included also a HTML help
              page.
(2) New:      Added SANLM filter, timing, intensity scaling, and file renaming batches
              before SPM long processing in cat_long_main (on the top) that also include
              different batch dependencies settings. Added refined SPM preprocessing
              settings to cat_run in case of job.extopts.new_release.
(3) Fixed:    Corrected WMHC and LAS parameter settings in the longitudinal average case
              in cat_long_main to avoid double corrections.
(4) Fixed:    Corrected bugs in cat_main_reportcmd and cat_vol_qa.
(5) Fixed:    Corrected bug in the brain-masking in case of internally interpolated
              longitudinal data with  in cat_main_updateSPM[1639] (also corrected a typo).
(6) New:      Extend cat_stat_check_cov to read native surface for longitudinal analysis.
(7) Fixed:    Small corrections in cat_run_job_APRGs to avoid reductions in very small
              brains.
(8) Fixed:    Added missing variable in cat_surf_createCS.
(9) Fixed:    Small corrections in cat_vol_groupwise_ls in case of deformation-average.
(10) Fixed:   Small correction in cat_vol_headtrimming if no new file is written.
(11) Fixed:   Corrected small bug in filename settings in cat_vol_qa.
(12) Fixed:   Corrected small rare bug in cat_run_job[1639].


------------------------------------------------------------------------
r1934 | gaser | 2022-01-28 10:48:48 +0100 (Fri, 28 Jan 2022) | 17 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cat_stat_spm2x.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_ui.m

(1) Changed: Updated help text and examples for cat_vol_slice_overlay_ui.m
             to cover all options.
(2) Changed: Extended cat_vol_slice_overlay to automatically define output
             images with either one column or one row.
             options.
(3) Changed: Updated help text in Makefile.
(4) Fixed:   Corrected bug in atlas output for cat_stat_spm2x where header
             information wasn't correct in some cases.


------------------------------------------------------------------------
r1933 | gaser | 2022-01-25 23:05:50 +0100 (Tue, 25 Jan 2022) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main_updateSPM1639.m
M       cat_stat_spm2x.m
M       cat_vol_set_com.m
M       html/cat.html

(1) Changed: Updated help text for cat_stat_set_com.m and removed output if
             not necessary.
(2) Fixed:   Output for cat_stat_spm2x was also written for empty results.


------------------------------------------------------------------------
r1932 | gaser | 2022-01-13 00:24:44 +0100 (Thu, 13 Jan 2022) | 30 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_amap.mexa64
M       cat_ornlm.mexa64
M       cat_plot_histogram.m
M       cat_sanlm.mexa64
M       cat_stat_spm2x.m
M       cat_vbdist.mexa64
M       cat_vol_downcut.mexa64
M       cat_vol_eidist.mexa64
M       cat_vol_genus0.mexa64
M       cat_vol_gradient3.mexa64
M       cat_vol_interp3f.mexa64
M       cat_vol_laplace3.mexa64
M       cat_vol_laplace3R.mexa64
M       cat_vol_localstat.mexa64
M       cat_vol_median3.mexa64
M       cat_vol_median3c.mexa64
M       cat_vol_pbtp.mexa64
M       cat_vol_simgrow.mexa64
M       html/cat.html

(1) Changed: Extended cat_stat_spm2x.m to handle null distribution files from
             TFCE toolbox.
(2) Changed: Extended cat_plot_histogram.m to treat effect size maps like
             T maps.
(3) Fixed:   Recompiled unix mex-files for compatibilty.


------------------------------------------------------------------------
r1931 | gaser | 2022-01-07 23:39:22 +0100 (Fri, 07 Jan 2022) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_main_reportfig.m

Fixed: Yet annother trial to handle unclear crashes in cat_main_reportfig.m.

------------------------------------------------------------------------
r1930 | gaser | 2022-01-07 19:19:19 +0100 (Fri, 07 Jan 2022) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       check_pipeline/batch_surface_pipeline.m
M       html/cat.html

(1) Changed: Updated batch_surface_pipeline.m to work with new check sample
             homogeneity tool.

------------------------------------------------------------------------
r1929 | gaser | 2022-01-07 18:06:57 +0100 (Fri, 07 Jan 2022) | 35 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_amap.mexa64
M       cat_batch_cat.sh
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_ornlm.mexa64
M       cat_sanlm.mexa64
M       cat_stat_check_SPM.m
M       cat_stat_check_cov.m
M       cat_vbdist.mexa64
M       cat_vol_downcut.mexa64
M       cat_vol_eidist.mexa64
M       cat_vol_genus0.mexa64
M       cat_vol_gradient3.mexa64
M       cat_vol_gradient3.mexmaci64
M       cat_vol_interp3f.mexa64
M       cat_vol_laplace3.mexa64
M       cat_vol_laplace3R.mexa64
M       cat_vol_localstat.mexa64
M       cat_vol_median3.mexa64
M       cat_vol_median3c.mexa64
M       cat_vol_pbtp.mexa64
M       cat_vol_simgrow.mexa64
M       html/cat.html

(1) Changed: Compiled Linux mex-files.
(2) Changed: Merged check sample homogeneity tools for volumes and surfaces.
(3) Changed: Changed GUI and batch files to only use one check sample
             homogeneity tool.
(4) Fixed:   Corrected handling of dartel export option in cat_batch_cat.sh.


------------------------------------------------------------------------
r1928 | gaser | 2022-01-07 17:54:20 +0100 (Fri, 07 Jan 2022) | 25 lines

Changed paths:
M       CHANGES.txt
M       cat_amap.mexw64
M       cat_io_colormaps.m
M       cat_ornlm.mexw64
M       cat_plot_histogram.m
M       cat_sanlm.mexw64
M       cat_vbdist.mexw64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexw64
M       cat_vol_pbtp.mexw64
M       cat_vol_simgrow.mexw64

Changed: Compiled Windows mex-files.
Changed: Prepared cat_plot_histogram.m to also support data as input and not
         only files.

------------------------------------------------------------------------
r1927 | dahnke | 2022-01-04 11:25:27 +0100 (Tue, 04 Jan 2022) | 32 lines

Changed paths:
M       CHANGES.txt
M       cat_io_lazy.m
M       cat_io_rerun.m
M       cat_long_main.m
M       cat_main_reportcmd.m
M       cat_main_reportfig.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1639.m

(1) Changed:  cat_run_lazy/rerun are now only verbose if no reprocessing is used.
(2) Changed:  Adapted longTPM filter strength parameter in cat_long_main
              and fixed strengthrong biased correction in single time points in
              cat_run to have the full benefit of the individual TPM.
(3) Fixed:    Small correction in cat_main_reportcmd.
(4) Changed:  Optimized background of the segmentation map in the CAT report in
              cat_main_reportfig.
(5) Fixed:    Multiple corrections in cat_main_updateSPM[1639] to handle the
              brainmasking in longitudinal processing.
(6) Changed:  Prepared stronger bias correction in longitudinal processing in
              cat_run (new_release).
(7) Fixed:    Corrected handling of background in longitudinal cases in
              cat_run_job[1639] to avoid problems due to the harder background
              definition that causes problems with the unified segmentation
              that was not able to get the real background values.
(8) Changed:  Optimized command line output of SPM tissue peaks in developer
              mode in cat_run_job[1639].


------------------------------------------------------------------------
r1926 | gaser | 2021-12-21 17:10:56 +0100 (Tue, 21 Dec 2021) | 38 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_amap.mex
M       cat_amap.mexmaci64
M       cat_io_rerun.m
M       cat_ornlm.mexmaci64
MM      cat_plot_histogram.m
M       cat_sanlm.mexmaci64
M       cat_stat_check_cov.m
M       cat_vbdist.mexmaci64
M       cat_vol_downcut.mexmaci64
M       cat_vol_eidist.mexmaci64
M       cat_vol_genus0.mexmaci64
M       cat_vol_gradient3.c
M       cat_vol_gradient3.mex
M       cat_vol_gradient3.mexmaci64
M       cat_vol_interp3f.mexmaci64
M       cat_vol_laplace3.mexmaci64
M       cat_vol_laplace3R.mexmaci64
M       cat_vol_localstat.mexmaci64
M       cat_vol_median3.mex
M       cat_vol_median3.mexmaci64
M       cat_vol_median3c.mexmaci64
M       cat_vol_pbtp.mexmaci64
M       cat_vol_pbtp2.mexmaci64
M       cat_vol_simgrow.mexmaci64
M       html/cat.html
M       internal/cat_vol_cMRegularizarNLM3D.mexmaci64

(1) Changed: Added cd to check_pipeline folder in Makefile.
(2) Fixed:   Corrected handling of filenames for meshes and nifti-files in
             cat_stat_check_cov.m
(3) Fixed:   Corrected deletion of hlps in cat_vol_gradient3.c.
(4) Fixed:   Added missing Amap.h again to cat_amap.c.
(5) Fixed:   Corrected check for missing "force" variable in cat_io_rerun.m.

------------------------------------------------------------------------
r1925 | dahnke | 2021-12-21 16:57:11 +0100 (Tue, 21 Dec 2021) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_amap.c
M       cat_io_lazy.m
M       cat_io_rerun.m
M       cat_vol_gradient3.c

(1) Fixed:   Corrected stupid bugs in cat_amap.c, cat_vol_gradient3.c,
             cat_io_rerun and cat_io_lazy.

------------------------------------------------------------------------
r1924 | dahnke | 2021-12-21 16:25:44 +0100 (Tue, 21 Dec 2021) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_median3.c
M       cat_vol_median3.m

(1) Fixed:   Corrected severe bug in cat_vol_median3.
(2) New:     Extended cat_vol_median3 to replace local NANs/INFs
             if the neighbors and mask allow it.


------------------------------------------------------------------------
r1923 | dahnke | 2021-12-20 17:53:15 +0100 (Mon, 20 Dec 2021) | 27 lines

Changed paths:
M       CHANGES.txt
M       cat_amap.c
M       cat_io_colormaps.m
M       cat_io_lazy.m
M       cat_io_rerun.m
M       cat_long_createTPM.m
M       cat_main_reportfig.m
M       cat_surf_create_TPM_hull_surface.m
M       cat_vbdist.c
M       cat_vol_downcut.c
M       cat_vol_eidist.c
M       cat_vol_gradient3.c
M       cat_vol_laplace3.c
M       cat_vol_laplace3R.c
M       cat_vol_pbtp.c
M       cat_vol_simgrow.c

(1) Fixed:   Prepared to manually free the memory in the c-functions of larger
             matrixes (currently commented).
(2) Changed: Refined settings in cat_long_createTPM and reset minimum class
             probability for further tests.
(3) Changed: Extended cat_io_lazy and cat_io_rerun by a force option to use this
             function in special save cases to avoid reprocessing of some files
             even in normal user modes, e.g. in cat_surf_create_TPM_hull_surface.


------------------------------------------------------------------------
r1922 | gaser | 2021-12-16 19:00:43 +0100 (Thu, 16 Dec 2021) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_conf_long.m
M       cat_plot_histogram.m
M       cat_stat_check_SPM.m
M       cat_stat_check_cov.m

(1) Changed: Imporved speed for nifti files in cat_stat_check_cov.m
(2) Changed: Added option to expert mode to save both longmodels in
             cat_conf_long.m.
(3) Changed: Added option to extract IQR values to CAT12 GUI.

------------------------------------------------------------------------
r1921 | dahnke | 2021-12-13 14:31:32 +0100 (Mon, 13 Dec 2021) | 40 lines

Changed paths:
M       Amap.c
M       Amap.h
M       CHANGES.txt
M       MrfPrior.c
M       cat_amap.c
M       cat_amap.m
M       cat_amap.mexmaci64
M       cat_io_csv.m
M       cat_io_xml.m
M       cat_main1639.m
M       cat_main_amap.m
M       cat_main_amap1639.m
M       cat_main_kamap.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_main_roi.m
M       cat_run.m
M       cat_run_job1639.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_create_TPM_hull_surface.m
M       cat_surf_surf2roi.m
M       cat_vol_qa.m
M       compile.m

(1) Fixed:   Corrected handling AMAP output variables in cat_main_[k]amap[1639].
             Added mean, std, and verb variables in cat_amap.c, MrfPrior.c, Amap.c/h
             cat_main_amap and cat_main_kamap.
(2) Fixed:   Further Octave correction in cat_surf_createCS[2] by full
             deactivation of surface correction collisions that creates a warning.
(3) Fixed:   As Shooting is yet not running under Octave, we switch to Dartel in
             cat_run and print a warning.
(4) Fixed:   Added further Octave corrections in cat_io_csv, cat_io_xml, compile,
             cat_main_reportstr, cat_main_reportfig, cat_surf_surf2roi.m, and cat_run.
(5) Fixed:   Corrected bugs under Octave for hull surface creation in
             cat_surf_create_TPM_hull_surface.
(6) Fixed:   Corrected missing definitions for Octave in cat_vol_qa.


------------------------------------------------------------------------
r1920 | gaser | 2021-12-13 14:01:39 +0100 (Mon, 13 Dec 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_io_colormaps.m
M       cat_plot_boxplot.m
A       cat_plot_histogram.m

(1) Changed: Added many new categorical colormaps to cat_io_colormaps.
(2) Changed: Changed default colormap in cat_plot_boxplot to nejm.
(3) Added:   Added new function to plot multiple histograms
             cat_plot_histograms.m

------------------------------------------------------------------------
r1919 | gaser | 2021-12-10 17:51:40 +0100 (Fri, 10 Dec 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_long.sh
M       cat_long_main.m
M       cat_stat_check_cov.m

(1) Changed: Updated help text for cat_batch_long.sh.
(2) Fixed:   Variable prep_str was not defined for all cases in
             cat_stat_check_cov.m.
(3) Fixed:   Corrected cat_long_main.m to allow saving of both longmodels.

------------------------------------------------------------------------
r1918 | gaser | 2021-12-09 16:32:10 +0100 (Thu, 09 Dec 2021) | 31 lines

Changed paths:
M       CHANGES.txt
M       cat_amap.mex
M       cat_batch_long.m
M       cat_batch_long.sh
M       cat_long_main.m
M       cat_main_amap.m
M       cat_main_amap1639.m
M       cat_ornlm.mex
M       cat_sanlm.mex
M       cat_stat_check_cov.m
M       cat_vbdist.mex
M       cat_vol_downcut.mex
M       cat_vol_eidist.mex
M       cat_vol_genus0.mex
M       cat_vol_gradient3.mex
M       cat_vol_interp3f.mex
M       cat_vol_laplace3.mex
M       cat_vol_laplace3R.mex
M       cat_vol_localstat.mex
M       cat_vol_median3.mex
M       cat_vol_median3c.mex
M       cat_vol_pbtp.mex
M       cat_vol_simgrow.mex
M       internal/cat_vol_cMRegularizarNLM3D.mex

(1) Changed: Corrected text interpreter in cat_stat_check_cov.m.
(2) Changed: Extended cat_long_main.m to correctly save both long. models.
(3) Changed: Many changes to cat_batch_long.sh and cat_batch_long.m to consider
             new options.

------------------------------------------------------------------------
r1917 | gaser | 2021-12-06 16:37:22 +0100 (Mon, 06 Dec 2021) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_long.m
M       cat_batch_long.sh
MM      cat_vol_pbtp2.m

Changed: Extended cat_batch_long.* by option to save affine registered
         segmentations for Dartel.


------------------------------------------------------------------------
r1916 | dahnke | 2021-12-02 10:51:53 +0100 (Thu, 02 Dec 2021) | 21 lines

Changed paths:
M       CHANGES.txt
M       cat_io_addwarning.m
M       cat_main_amap.m
M       cat_main_amap1639.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m
M       cat_vol_resize.m

(1) Fixed:   Corrected bugs in Octave in cat_main_amap[1639] because
             Octaves evalc function does not catch the output of the
             called AMAP c-function.
(2) Fixed:   Corrected Octave char warning in cat_io_addwarning and
             corrected output behavior that differs from Matlab.
(3) Fixed:   Corrected Octave meshgrid in cat_vol_resize.m
(4) Fixed:   Replaced outdated call of flipdim by flip in cat_surf_fun.
(5) Fixed:   Skipping of the second fine collision correction in
             cat_surf_createCS[2] in Octave.


------------------------------------------------------------------------
r1915 | gaser | 2021-11-30 16:28:08 +0100 (Tue, 30 Nov 2021) | 17 lines

Changed paths:
M       Amap.c
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_vol_downcut.c
M       cat_vol_pbtp.c
M       cat_vol_pbtp2.c
M       cat_vol_resize.m
M       cat_vol_simgrow.c
M       compile.m
M       html/cat.html
M       html/cat_starting.html

(1) Changed: Added OCTAVE Macro to Amap.c to allow running original code under
             Matlab.
(2) Changed: Extended help text for Quick start guide.

------------------------------------------------------------------------
r1914 | dahnke | 2021-11-30 14:40:04 +0100 (Tue, 30 Nov 2021) | 69 lines

Changed paths:
M       Amap.c
M       CHANGES.txt
M       Kmeans.c
M       MrfPrior.c
M       Pve.c
M       cat_amap.c
M       cat_amap.m
M       cat_amap.mex
M       cat_amap.mexmaci64
M       cat_main_amap.m
M       cat_main_amap1639.m
M       cat_main_kamap.m
M       cat_ornlm.mex
M       cat_ornlm.mexmaci64
M       cat_sanlm.mex
M       cat_sanlm.mexmaci64
M       cat_vbdist.mex
M       cat_vbdist.mexmaci64
M       cat_vol_ROIval.c
M       cat_vol_ROIval.mexmaci64
M       cat_vol_downcut.mex
M       cat_vol_downcut.mexmaci64
M       cat_vol_eidist.mex
M       cat_vol_eidist.mexmaci64
D       cat_vol_eikonal3.c
D       cat_vol_eikonal3.m
M       cat_vol_genus0.mex
M       cat_vol_genus0.mexmaci64
M       cat_vol_gradient3.mex
M       cat_vol_gradient3.mexmaci64
M       cat_vol_interp3f.mex
M       cat_vol_interp3f.mexmaci64
M       cat_vol_laplace3.c
M       cat_vol_laplace3.mex
M       cat_vol_laplace3.mexmaci64
M       cat_vol_laplace3R.mex
M       cat_vol_laplace3R.mexmaci64
M       cat_vol_localstat.m
M       cat_vol_localstat.mex
M       cat_vol_localstat.mexmaci64
M       cat_vol_median3.c
M       cat_vol_median3.mex
M       cat_vol_median3.mexmaci64
M       cat_vol_median3c.c
M       cat_vol_median3c.mex
M       cat_vol_median3c.mexmaci64
M       cat_vol_pbtp.c
M       cat_vol_pbtp.mex
M       cat_vol_pbtp.mexmaci64
M       cat_vol_pbtp2.c
A       cat_vol_pbtp2.m
M       cat_vol_pbtp2.mexmaci64
M       cat_vol_simgrow.mex
M       cat_vol_simgrow.mexmaci64
M       compile.m
M       internal/cat_vol_cMRegularizarNLM3D.mex
M       internal/cat_vol_cMRegularizarNLM3D.mexmaci64

(1) Deleted:   Remove unused function cat_vol_eikonal3.c.
(2) Fixed:     Corrected cat_vol_ROIval.c, cat_vol_pbtp2.c.
(3) Fixed:     Corrected bugs in cat_vol_laplace3.c and
               cat_vol_median3.c.
(4) Fixed:     Corrected octave bugs in compile.
(5) Fixed:     Corrected octave issues in cat_amap.c,
               Amap.c, kmeans.c, MrfPrior.c, Pve.c and
               cat_main_amap[1639].


------------------------------------------------------------------------
r1913 | dahnke | 2021-11-28 21:44:47 +0100 (Sun, 28 Nov 2021) | 23 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_downcut.c
M       cat_vol_downcut.mexmaci64
M       cat_vol_gradient3.c
M       cat_vol_gradient3.mexmaci64
M       cat_vol_median3.c
M       cat_vol_median3.m
M       cat_vol_median3.mexmaci64
M       cat_vol_median3c.c
M       cat_vol_median3c.m
M       cat_vol_median3c.mexmaci64
M       cat_vol_pbtp.c
M       cat_vol_pbtp.mexmaci64

(1) Fixed:   Corrected Octave bugs and added examples in documentation in
               cat_vol_laplace3(R), cat_vol_simgrow, cat_vol_gradient3,
               cat_vol_eikonal3, cat_vol_eidist, cat_vol_downcut,
               cat_vol_pbtp, and cat_vol_median3(c).
(2) Fixed:   Small adaptions for display function ds.
(3) New:     Added normalization parameter to cat_vol_gradient3.


------------------------------------------------------------------------
r1912 | dahnke | 2021-11-27 15:14:31 +0100 (Sat, 27 Nov 2021) | 30 lines

Changed paths:
M       CHANGES.txt
M       cat_vbdist.c
M       cat_vol_downcut.c
M       cat_vol_downcut.m
M       cat_vol_downcut.mexmaci64
M       cat_vol_eidist.c
M       cat_vol_eidist.m
M       cat_vol_eidist.mexmaci64
M       cat_vol_eikonal3.c
M       cat_vol_eikonal3.m
M       cat_vol_eikonal3.mexmaci64
M       cat_vol_laplace3.c
M       cat_vol_laplace3.m
M       cat_vol_laplace3.mexmaci64
M       cat_vol_laplace3R.c
M       cat_vol_laplace3R.m
M       cat_vol_laplace3R.mexmaci64
M       cat_vol_localstat.c
M       cat_vol_simgrow.c
M       cat_vol_simgrow.m
M       cat_vol_simgrow.mexmaci64
M       ds.m

(1) Fixed:   Corrected Octave bugs and added examples in documentation in
               cat_vol_laplace3(R), cat_vol_simgrow, cat_vol_gradient3,
               cat_vol_eikonal3, cat_vol_eidist, cat_vol_downcut.
(2) Fixed:   Small adaptions for display function ds.


------------------------------------------------------------------------
r1911 | dahnke | 2021-11-26 15:33:25 +0100 (Fri, 26 Nov 2021) | 44 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_main.m
M       cat_main1639.m
M       cat_run_job_APRGs.m
M       cat_surf_fun.m
M       cat_vbdist.c
M       cat_vbdist.m
M       cat_vbdist.mexmaci64
M       cat_vol_div.m
M       cat_vol_grad.m
M       cat_vol_localstat.c
M       cat_vol_localstat.m
M       cat_vol_localstat.mexmaci64
M       compile.m
M       ds.m
M       spm_cat12.m

(1) Fixed:   Added missing variable in catch-block in cat_main.
(2) Fixed:   Corrected octave bugs in cat_vbdist and cat_vol_localstat.
             Updated documentation and help.
(3) Fixed:   Corrected median estimation in cat_vol_localstat that is
             currently not used.
(4) Changed: Throw error message in case of experimental histogram functions
             that are not used and seams not not work in a proper way.
(5) New:     Added further functionality to cat_vol_localstat, such as
             iterations, definition of mask area, handling of zeros,
             that are in line with previous use.
(6) New:     Added subfunction to debugging display function ds.
(7) Changed: Small changes in documentation in cat12 and spm_cat12.
(8) Fixed:   Corrected small bug in inactive path in cat_main1639.
(9) Changed: Did not changed undefined output from FLT_MAX to INFINITY
             in cat_vbdist because this may cause to many problems. Although,
             this changes are tiny such as in cat_run_job_APRGs, there are
             too many cases where it may cause further problems that are
             currently running.
(10) New:    Added normalization parameter and new normalization function
             in cat_vol_div that is not used by default.
(11) New:    Added new functionality in cat_vol_grad to handle NANs and to
             normalize the gradients. Added further documentation.



------------------------------------------------------------------------
r1910 | gaser | 2021-11-26 14:47:25 +0100 (Fri, 26 Nov 2021) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_check_cov.m
M       cat_stat_confplot_spm.m

Changed: Updated search for corresponding xml-files in cat_stat_check_cov.m

------------------------------------------------------------------------
r1909 | gaser | 2021-11-24 12:19:25 +0100 (Wed, 24 Nov 2021) | 32 lines

Changed paths:
M       CHANGES.txt
M       cat_amap.mex
M       cat_ornlm.mex
M       cat_sanlm.mex
M       cat_stat_check_cov.m
M       cat_vbdist.mex
M       cat_vol_downcut.c
M       cat_vol_downcut.mex
M       cat_vol_eidist.c
M       cat_vol_eidist.mex
M       cat_vol_eikonal3.c
M       cat_vol_genus0.mex
M       cat_vol_gradient3.c
M       cat_vol_gradient3.mex
M       cat_vol_interp3f.mex
M       cat_vol_laplace3.c
M       cat_vol_laplace3.mex
M       cat_vol_laplace3R.c
M       cat_vol_laplace3R.mex
M       cat_vol_localstat.mex
M       cat_vol_median3.mex
M       cat_vol_median3c.mex
M       cat_vol_pbtp.mex
M       cat_vol_pbtp2.c
M       cat_vol_simgrow.c
M       cat_vol_simgrow.mex
M       internal/cat_vol_cMRegularizarNLM3D.mex

(1) Changed: Move on with cov-check if report files are incomplete.
(2) Changed: Modified ind2sub subfunction for many c-files.

------------------------------------------------------------------------
r1908 | gaser | 2021-11-22 12:15:04 +0100 (Mon, 22 Nov 2021) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_confplot_spm.m
M       cat_system.m
M       html/cat.html
M       standalone/cat_standalone_segment_long.m

(1) Changed: Added check for nuisance interactions to cat_stat_confplot_spm.m
             that will not work to plot raw data.
(2) Fixed:   Variable catdir was missing in cat_system.m.
(3) Fixed:   Removed UNDEFINED-field from cat_standalone_segment_long.m that
             caused crashes ins standalone mode for longitudinal data (thanks
             to Felix Hofstaedter for pointing to that error).

------------------------------------------------------------------------
r1907 | gaser | 2021-11-17 23:17:30 +0100 (Wed, 17 Nov 2021) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m

Fixed: Removed wrong interpreter option in cat_surf_results.m.

------------------------------------------------------------------------
r1906 | gaser | 2021-11-16 17:55:46 +0100 (Tue, 16 Nov 2021) | 17 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_check_system_output.m
M       cat_conf_tools.m
M       cat_stat_confplot_spm.m
M       cat_surf_map_atlas.m
M       cat_system.m
M       html/cat.html

(1) Changed: Added Quick Start Guide to cat_stat_confplot_spm.m.
(2) Changed: Added additional output parameter to cat_system.m and
             cat_check_system_output.m.
(3) Changed: Updated help text and GUI names for cat_conf_tools.m and cat12.m.
(4) Fixed:   Added missing output parameter to cat_surf_map_atlas.m

------------------------------------------------------------------------
r1905 | gaser | 2021-11-15 21:08:56 +0100 (Mon, 15 Nov 2021) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_main_reportfig.m

Changed: Yet another trial to prevent errors in cat_main_reportfig.m.

------------------------------------------------------------------------
r1904 | gaser | 2021-11-02 14:58:07 +0100 (Tue, 02 Nov 2021) | 20 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_plot_boxplot.m
M       cat_run_job1639.m
M       cat_run_newcatch.m
M       cat_surf_results.m
M       cat_surf_vol2surf.m
M       cat_vol_groupwise_ls.m
M       cat_vol_qa.m
M       html/cat.html

(1) Changed: Considered display-less occurance of errors in cat_run_newcatch.m.
(2) Changed: Some smaller changes for compatibiliy.
(3) Changed: Changed text interpreter to "none" in cat_surf_results.m and
             again modified clim option.
(4) Changed: Removed output parameters for cat_system function in
             cat_surf_vol2surf.m.
(5) Fixed:   Corrected bug in size comparison in cat_vol_qa.m.

------------------------------------------------------------------------
r1903 | dahnke | 2021-11-02 09:09:12 +0100 (Tue, 02 Nov 2021) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_vol_qa.m

(1) Fixed:   Corrected tiny bug due to imaginary values in cat_vol_qa.
(2) New:     Added longitudinal skull-stripping cases in cat_main_updateSPM[1639].
(3) New:     Added backup routine for cat_spm_preproc8 in cat_run_job[1639].


------------------------------------------------------------------------
r1902 | dahnke | 2021-10-30 16:32:01 +0200 (Sat, 30 Oct 2021) | 34 lines

Changed paths:
M       CHANGES.txt
M       cat_io_lazy.m
M       cat_io_rerun.m
M       cat_long_createTPM.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_LAS2.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_surf_createCS2.m
M       cat_surf_create_TPM_hull_surface.m
M       cat_vol_headtrimming.m
M       cat_vol_partvol1639.m
M       cat_vol_sanlm.m
M       ds.m
M       templates_surfaces/bh.headbrain.TPM.gii

(1) Fixed:      Corrected bug in cat_io_run/lazy that avoid reprocessing of
                files with equal age (only used in developer mode).
(2) Fixed:      Corrected bug due to missing lesion variable in cat_main1639
                that is already fixed in cat_main.
(3) Fixed:      Corrected handling of missing variable in cat_main_LAS2.
(4) Fixed:      Further corrections to handle miss-aligned backgrounds in
                longitudinal processing in cat_main_upateSPM[1639].
                Further changes in cat_long_createTPM.
(5) Fixed:      Corrected handling of variables in backup routine of
                cat_run_job[1639].
(6) Fixed:      Corrected bug in cat_surf_createCS2.
(7) Fixed:      Corrected default setting of lazy/rerun option in
                cat_vol_headtrimming.

------------------------------------------------------------------------
r1901 | gaser | 2021-10-26 12:25:52 +0200 (Tue, 26 Oct 2021) | 32 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_long.m
M       cat_check_system_output.m
M       cat_main_reportfig.m
M       cat_surf_avg.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_flipsides.m
M       cat_surf_fun.m
M       cat_surf_gyrification.m
M       cat_surf_map_atlas.m
M       cat_surf_parameters.m
M       cat_surf_renderv.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
M       cat_surf_results.m
M       cat_surf_smooth.m
M       cat_surf_surf2roi.m
M       cat_surf_vol2surf.m
M       cat_system.m
M       check_pipeline.sh
M       html/cat.html
M       spm_cat12.m

(1) Changed: Integrated cat_check_system_output.m into cat_system.m to make
             system calls easier.
(2) Changed: Added check whether binaries can be executed to cat_system.m.
(3) Changed: Changed check for render view in check_pipeline.sh.
(4) Fixed:   Removed clearing of cat_defaults in cat_batch_long.m.

------------------------------------------------------------------------
r1900 | gaser | 2021-10-25 11:13:19 +0200 (Mon, 25 Oct 2021) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_confplot_spm.m

Fixed: Restricted plots of covariates in cat_stat_confplot_spm.m.

------------------------------------------------------------------------
r1899 | gaser | 2021-10-25 10:17:10 +0200 (Mon, 25 Oct 2021) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_main_LAS2.m
M       cat_main_LASs.m
M       cat_stat_spm2x.m
M       cat_surf_results.m
M       cat_vol_slice_overlay.m

(1) Changed: Replaced "Size" by "Cluster-Size" in some functions to better
             describe that parameter.
(2) Changed: Set text interpreter to "none" in cat_surf_results.m for data tips.
(3) Fixed:   Corrected some typos.


------------------------------------------------------------------------
r1898 | gaser | 2021-10-25 09:12:48 +0200 (Mon, 25 Oct 2021) | 13 lines

Changed paths:
M       CHANGES.txt
MM      cat_roi_values2surf.m
M       cat_stat_analyze_ROIs.m
M       cat_stat_confplot_spm.m

(1) Changed: Added check for F-contrasts for effects of interest to
             cat_stat_confplot_spm.m to prevent plotting of raw data for
             that case.
(2) Changed: Added a break if no xml-files were found to save time in
             cat_stat_analyze_ROIs.m.


------------------------------------------------------------------------
r1897 | dahnke | 2021-10-24 10:51:16 +0200 (Sun, 24 Oct 2021) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_main_LAS2.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       ds.m

(1) Fixed:      Corrected bug in LAS2 in case of empty background class.
(2) Fixed:      Corrected bug in longitudinal processing of single timepoints
                with empty backgrounds in cat_main_updateSPM[1639].






------------------------------------------------------------------------
r1896 | gaser | 2021-10-22 15:42:07 +0200 (Fri, 22 Oct 2021) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_surf_fun.m
M       cat_surf_results.m
M       cat_vol_slice_overlay.m
M       compile.m

(1) Changed: Added compilation for octave to compile.m.
(2) Fixed:   Added missing function handle to cat_vol_slice_overlay.m.
(3) Fixed:   Corrected use of clim in cat_surf_results.m and made some smaller
             changes for compatibility.
(4) Fixed:   Corrected typo in cat12.m and made some smaller changes for
             compatibility.


------------------------------------------------------------------------
r1895 | gaser | 2021-10-15 01:49:00 +0200 (Fri, 15 Oct 2021) | 10 lines

Changed paths:
M       CHANGES.txt

(1) Added:   Added new function cat_roi_values2surf.m to map ROI values to
             surface file.
(2) Changed: Simplified some code in cat_surf_surf2roi.m.
(3) Fixed:   Corrected call of 'clim' in cat_surf_results.m
(4) Fixed:   Corrected typo in cat_stat_analyze_ROIs.m


------------------------------------------------------------------------
r1894 | gaser | 2021-10-15 01:45:55 +0200 (Fri, 15 Oct 2021) | 93 lines

Changed paths:
 M      CAT.glnx86/CAT_3dVol2Surf
 M      CAT.glnx86/CAT_AddValuesToSurf
 M      CAT.glnx86/CAT_AverageSurfaces
 M      CAT.glnx86/CAT_BlurSurfHK
 M      CAT.glnx86/CAT_Central2Pial
 M      CAT.glnx86/CAT_DeformSurf
 M      CAT.glnx86/CAT_DumpCurv
 M      CAT.glnx86/CAT_DumpSurfArea
 M      CAT.glnx86/CAT_DumpSurfaceRatio
 M      CAT.glnx86/CAT_FixTopology
 M      CAT.glnx86/CAT_FractalDimension
 M      CAT.glnx86/CAT_Hausdorff
 M      CAT.glnx86/CAT_Isometize
 M      CAT.glnx86/CAT_MarkDefects
 M      CAT.glnx86/CAT_RefineMesh
 M      CAT.glnx86/CAT_ResampleSphericalSurf
 M      CAT.glnx86/CAT_ResampleSphericalSurfSPH
 M      CAT.glnx86/CAT_ResampleSurf
 M      CAT.glnx86/CAT_SelfIntersect
 M      CAT.glnx86/CAT_SeparatePolygon
 M      CAT.glnx86/CAT_SmoothConvexity
 M      CAT.glnx86/CAT_SulcusDepth
 M      CAT.glnx86/CAT_Surf2Sphere
 M      CAT.glnx86/CAT_Surf2Vol
 M      CAT.glnx86/CAT_SurfDistance
 M      CAT.glnx86/CAT_WarpSurf
 M      CAT.maci64/CAT_3dVol2Surf
 M      CAT.maci64/CAT_AddValuesToSurf
 M      CAT.maci64/CAT_AverageSurfaces
 M      CAT.maci64/CAT_BlurSurfHK
 M      CAT.maci64/CAT_Central2Pial
 M      CAT.maci64/CAT_DeformSurf
 M      CAT.maci64/CAT_DumpCurv
 M      CAT.maci64/CAT_DumpSurfArea
 M      CAT.maci64/CAT_DumpSurfaceRatio
 M      CAT.maci64/CAT_FixTopology
 M      CAT.maci64/CAT_FractalDimension
 M      CAT.maci64/CAT_Hausdorff
 M      CAT.maci64/CAT_Isometize
 M      CAT.maci64/CAT_MarkDefects
 M      CAT.maci64/CAT_RefineMesh
 M      CAT.maci64/CAT_ResampleSphericalSurf
 M      CAT.maci64/CAT_ResampleSphericalSurfSPH
 M      CAT.maci64/CAT_ResampleSurf
 M      CAT.maci64/CAT_SelfIntersect
 M      CAT.maci64/CAT_SeparatePolygon
 M      CAT.maci64/CAT_SmoothConvexity
 M      CAT.maci64/CAT_SulcusDepth
 M      CAT.maci64/CAT_Surf2Sphere
 M      CAT.maci64/CAT_Surf2Vol
 M      CAT.maci64/CAT_SurfDistance
 M      CAT.maci64/CAT_WarpSurf
 M      CAT.w32/CAT_3dVol2Surf.exe
 M      CAT.w32/CAT_AddValuesToSurf.exe
 M      CAT.w32/CAT_AverageSurfaces.exe
 M      CAT.w32/CAT_BlurSurfHK.exe
 M      CAT.w32/CAT_Central2Pial.exe
 M      CAT.w32/CAT_DeformSurf.exe
 M      CAT.w32/CAT_DumpCurv.exe
 M      CAT.w32/CAT_DumpSurfArea.exe
 M      CAT.w32/CAT_DumpSurfaceRatio.exe
 M      CAT.w32/CAT_FixTopology.exe
 M      CAT.w32/CAT_FractalDimension.exe
 M      CAT.w32/CAT_Hausdorff.exe
 M      CAT.w32/CAT_Isometize.exe
 M      CAT.w32/CAT_MarkDefects.exe
 M      CAT.w32/CAT_RefineMesh.exe
 M      CAT.w32/CAT_ResampleSphericalSurf.exe
 M      CAT.w32/CAT_ResampleSphericalSurfSPH.exe
 M      CAT.w32/CAT_ResampleSurf.exe
 M      CAT.w32/CAT_SelfIntersect.exe
 M      CAT.w32/CAT_SeparatePolygon.exe
 M      CAT.w32/CAT_SmoothConvexity.exe
 M      CAT.w32/CAT_SulcusDepth.exe
 M      CAT.w32/CAT_Surf2Sphere.exe
 M      CAT.w32/CAT_Surf2Vol.exe
 M      CAT.w32/CAT_SurfDistance.exe
 M      CAT.w32/CAT_WarpSurf.exe
M       CHANGES.txt
M       cat_roi_roi2surf.m
A       cat_roi_values2surf.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_results.m
M       cat_surf_surf2roi.m

(1) Added:   Added new function cat_roi_values2surf.m to map ROI values to
             surface file.
(2) Changed: Simplified some code in cat_surf_surf2roi.m.
(3) Fixed:   Corrected call of 'clim' in cat_surf_results.m
(4) Fixed:   Corrected typo in cat_stat_analyze_ROIs.m


------------------------------------------------------------------------
r1893 | gaser | 2021-10-13 19:20:43 +0200 (Wed, 13 Oct 2021) | 10 lines

Changed paths:
M       CHANGES.txt
M       cp_binaries.sh

(1) Fixed:   Corrected recognition of ROI use in tbx_cfg_cat.m
(2) Fixed:   Corrected use of original labelmaps in cat_surf_render2.m.
(3) Fixed:   Corrected YTickLabels in cat_surf_render2.m for annot files.
(4) Fixed:   Corrected deletion of temporary files in longitudinal pipeline.


------------------------------------------------------------------------
r1892 | gaser | 2021-10-13 19:15:38 +0200 (Wed, 13 Oct 2021) | 35 lines

Changed paths:
M       CAT.glnx86/CAT_3dVol2Surf
M       CAT.maci64/CAT_3dVol2Surf
M       CAT.w32/CAT_3dVol2Surf.exe
M       CAT.w32/CAT_AddValuesToSurf.exe
M       CAT.w32/CAT_AverageSurfaces.exe
M       CAT.w32/CAT_BlurSurfHK.exe
M       CAT.w32/CAT_Central2Pial.exe
M       CAT.w32/CAT_DeformSurf.exe
M       CAT.w32/CAT_DumpCurv.exe
M       CAT.w32/CAT_DumpSurfArea.exe
M       CAT.w32/CAT_DumpSurfaceRatio.exe
M       CAT.w32/CAT_FixTopology.exe
M       CAT.w32/CAT_FractalDimension.exe
M       CAT.w32/CAT_Hausdorff.exe
M       CAT.w32/CAT_Isometize.exe
M       CAT.w32/CAT_MarkDefects.exe
M       CAT.w32/CAT_RefineMesh.exe
M       CAT.w32/CAT_ResampleSphericalSurf.exe
M       CAT.w32/CAT_ResampleSphericalSurfSPH.exe
M       CAT.w32/CAT_ResampleSurf.exe
M       CAT.w32/CAT_SelfIntersect.exe
M       CAT.w32/CAT_SeparatePolygon.exe
M       CAT.w32/CAT_SmoothConvexity.exe
M       CAT.w32/CAT_SulcusDepth.exe
M       CAT.w32/CAT_Surf2Sphere.exe
M       CAT.w32/CAT_Surf2Vol.exe
M       CAT.w32/CAT_SurfDistance.exe
M       CAT.w32/CAT_WarpSurf.exe
M       CHANGES.txt
 M      cp_binaries.sh

(1) Changed: Updated binaries.


------------------------------------------------------------------------
r1891 | gaser | 2021-10-13 19:09:04 +0200 (Wed, 13 Oct 2021) | 87 lines

Changed paths:
A       CAT.glnx86
A       CAT.glnx86/CAT_3dVol2Surf
A       CAT.glnx86/CAT_AddValuesToSurf
A       CAT.glnx86/CAT_AverageSurfaces
A       CAT.glnx86/CAT_BlurSurfHK
A       CAT.glnx86/CAT_Central2Pial
A       CAT.glnx86/CAT_DeformSurf
A       CAT.glnx86/CAT_DumpCurv
A       CAT.glnx86/CAT_DumpSurfArea
A       CAT.glnx86/CAT_DumpSurfaceRatio
A       CAT.glnx86/CAT_FixTopology
A       CAT.glnx86/CAT_FractalDimension
A       CAT.glnx86/CAT_Hausdorff
A       CAT.glnx86/CAT_Isometize
A       CAT.glnx86/CAT_MarkDefects
A       CAT.glnx86/CAT_RefineMesh
A       CAT.glnx86/CAT_ResampleSphericalSurf
A       CAT.glnx86/CAT_ResampleSphericalSurfSPH
A       CAT.glnx86/CAT_ResampleSurf
A       CAT.glnx86/CAT_SelfIntersect
A       CAT.glnx86/CAT_SeparatePolygon
A       CAT.glnx86/CAT_SmoothConvexity
A       CAT.glnx86/CAT_SulcusDepth
A       CAT.glnx86/CAT_Surf2Sphere
A       CAT.glnx86/CAT_Surf2Vol
A       CAT.glnx86/CAT_SurfDistance
A       CAT.glnx86/CAT_WarpSurf
A       CAT.maci64
A       CAT.maci64/CAT_3dVol2Surf
A       CAT.maci64/CAT_AddValuesToSurf
A       CAT.maci64/CAT_AverageSurfaces
A       CAT.maci64/CAT_BlurSurfHK
A       CAT.maci64/CAT_Central2Pial
A       CAT.maci64/CAT_DeformSurf
A       CAT.maci64/CAT_DumpCurv
A       CAT.maci64/CAT_DumpSurfArea
A       CAT.maci64/CAT_DumpSurfaceRatio
A       CAT.maci64/CAT_FixTopology
A       CAT.maci64/CAT_FractalDimension
A       CAT.maci64/CAT_Hausdorff
A       CAT.maci64/CAT_Isometize
A       CAT.maci64/CAT_MarkDefects
A       CAT.maci64/CAT_RefineMesh
A       CAT.maci64/CAT_ResampleSphericalSurf
A       CAT.maci64/CAT_ResampleSphericalSurfSPH
A       CAT.maci64/CAT_ResampleSurf
A       CAT.maci64/CAT_SelfIntersect
A       CAT.maci64/CAT_SeparatePolygon
A       CAT.maci64/CAT_SmoothConvexity
A       CAT.maci64/CAT_SulcusDepth
A       CAT.maci64/CAT_Surf2Sphere
A       CAT.maci64/CAT_Surf2Vol
A       CAT.maci64/CAT_SurfDistance
A       CAT.maci64/CAT_WarpSurf
A       CAT.w32
A       CAT.w32/CAT_3dVol2Surf.exe
A       CAT.w32/CAT_AddValuesToSurf.exe
A       CAT.w32/CAT_AverageSurfaces.exe
A       CAT.w32/CAT_BlurSurfHK.exe
A       CAT.w32/CAT_Central2Pial.exe
A       CAT.w32/CAT_DeformSurf.exe
A       CAT.w32/CAT_DumpCurv.exe
A       CAT.w32/CAT_DumpSurfArea.exe
A       CAT.w32/CAT_DumpSurfaceRatio.exe
A       CAT.w32/CAT_FixTopology.exe
A       CAT.w32/CAT_FractalDimension.exe
A       CAT.w32/CAT_Hausdorff.exe
A       CAT.w32/CAT_Isometize.exe
A       CAT.w32/CAT_MarkDefects.exe
A       CAT.w32/CAT_RefineMesh.exe
A       CAT.w32/CAT_ResampleSphericalSurf.exe
A       CAT.w32/CAT_ResampleSphericalSurfSPH.exe
A       CAT.w32/CAT_ResampleSurf.exe
A       CAT.w32/CAT_SelfIntersect.exe
A       CAT.w32/CAT_SeparatePolygon.exe
A       CAT.w32/CAT_SmoothConvexity.exe
A       CAT.w32/CAT_SulcusDepth.exe
A       CAT.w32/CAT_Surf2Sphere.exe
A       CAT.w32/CAT_Surf2Vol.exe
A       CAT.w32/CAT_SurfDistance.exe
A       CAT.w32/CAT_WarpSurf.exe
M       CHANGES.txt

(1) Changed: Added missing binaries.


------------------------------------------------------------------------
r1890 | gaser | 2021-10-13 19:06:57 +0200 (Wed, 13 Oct 2021) | 96 lines

Changed paths:
D       CAT.glnx86
D       CAT.glnx86/CAT_3dVol2Surf
D       CAT.glnx86/CAT_AddValuesToSurf
D       CAT.glnx86/CAT_AverageSurfaces
D       CAT.glnx86/CAT_BlurSurfHK
D       CAT.glnx86/CAT_Central2Pial
D       CAT.glnx86/CAT_DeformSurf
D       CAT.glnx86/CAT_DumpCurv
D       CAT.glnx86/CAT_DumpSurfArea
D       CAT.glnx86/CAT_DumpSurfaceRatio
D       CAT.glnx86/CAT_FixTopology
D       CAT.glnx86/CAT_FractalDimension
D       CAT.glnx86/CAT_Hausdorff
D       CAT.glnx86/CAT_Isometize
D       CAT.glnx86/CAT_MarkDefects
D       CAT.glnx86/CAT_RefineMesh
D       CAT.glnx86/CAT_ResampleSphericalSurf
D       CAT.glnx86/CAT_ResampleSphericalSurfSPH
D       CAT.glnx86/CAT_ResampleSurf
D       CAT.glnx86/CAT_SelfIntersect
D       CAT.glnx86/CAT_SeparatePolygon
D       CAT.glnx86/CAT_SmoothConvexity
D       CAT.glnx86/CAT_SulcusDepth
D       CAT.glnx86/CAT_Surf2Sphere
D       CAT.glnx86/CAT_Surf2Vol
D       CAT.glnx86/CAT_SurfDistance
D       CAT.glnx86/CAT_WarpSurf
D       CAT.maci64
D       CAT.maci64/CAT_3dVol2Surf
D       CAT.maci64/CAT_AddValuesToSurf
D       CAT.maci64/CAT_AverageSurfaces
D       CAT.maci64/CAT_BlurSurfHK
D       CAT.maci64/CAT_Central2Pial
D       CAT.maci64/CAT_DeformSurf
D       CAT.maci64/CAT_DumpCurv
D       CAT.maci64/CAT_DumpSurfArea
D       CAT.maci64/CAT_DumpSurfaceRatio
D       CAT.maci64/CAT_FixTopology
D       CAT.maci64/CAT_FractalDimension
D       CAT.maci64/CAT_Hausdorff
D       CAT.maci64/CAT_Isometize
D       CAT.maci64/CAT_MarkDefects
D       CAT.maci64/CAT_RefineMesh
D       CAT.maci64/CAT_ResampleSphericalSurf
D       CAT.maci64/CAT_ResampleSphericalSurfSPH
D       CAT.maci64/CAT_ResampleSurf
D       CAT.maci64/CAT_SelfIntersect
D       CAT.maci64/CAT_SeparatePolygon
D       CAT.maci64/CAT_SmoothConvexity
D       CAT.maci64/CAT_SulcusDepth
D       CAT.maci64/CAT_Surf2Sphere
D       CAT.maci64/CAT_Surf2Vol
D       CAT.maci64/CAT_SurfDistance
D       CAT.maci64/CAT_WarpSurf
D       CAT.w32
D       CAT.w32/CAT_3dVol2Surf.exe
D       CAT.w32/CAT_AddValuesToSurf.exe
D       CAT.w32/CAT_AverageSurfaces.exe
D       CAT.w32/CAT_BlurSurfHK.exe
D       CAT.w32/CAT_Central2Pial.exe
D       CAT.w32/CAT_DeformSurf.exe
D       CAT.w32/CAT_DumpCurv.exe
D       CAT.w32/CAT_DumpSurfArea.exe
D       CAT.w32/CAT_DumpSurfaceRatio.exe
D       CAT.w32/CAT_FixTopology.exe
D       CAT.w32/CAT_FractalDimension.exe
D       CAT.w32/CAT_Hausdorff.exe
D       CAT.w32/CAT_Isometize.exe
D       CAT.w32/CAT_MarkDefects.exe
D       CAT.w32/CAT_RefineMesh.exe
D       CAT.w32/CAT_ResampleSphericalSurf.exe
D       CAT.w32/CAT_ResampleSphericalSurfSPH.exe
D       CAT.w32/CAT_ResampleSurf.exe
D       CAT.w32/CAT_SelfIntersect.exe
D       CAT.w32/CAT_SeparatePolygon.exe
D       CAT.w32/CAT_SmoothConvexity.exe
D       CAT.w32/CAT_SulcusDepth.exe
D       CAT.w32/CAT_Surf2Sphere.exe
D       CAT.w32/CAT_Surf2Vol.exe
D       CAT.w32/CAT_SurfDistance.exe
D       CAT.w32/CAT_WarpSurf.exe
M       CHANGES.txt
M       cat_install_tfce.m
M       cat_surf_createCS2.m
M       cat_update.m
M       cat_vol_morph.m
A       cp_binaries.sh

(1) Changed: Updated binaries.
(2) Fixed:   Corrected help text in cat_vol_morph.c.
(3) Fixed:   Added check for toolbox_path_cache command to cat_update.m and
             cat_install_tfce.m.
(4) Fixed:   Corrected handling of missing job variable in cat_surf_createCS2.m.


------------------------------------------------------------------------
r1889 | gaser | 2021-10-13 16:53:31 +0200 (Wed, 13 Oct 2021) | 119 lines

Changed paths:
 M      CAT.glnx86/CAT_3dVol2Surf
 M      CAT.glnx86/CAT_AddValuesToSurf
 M      CAT.glnx86/CAT_AverageSurfaces
 M      CAT.glnx86/CAT_BlurSurfHK
 M      CAT.glnx86/CAT_Central2Pial
 M      CAT.glnx86/CAT_DeformSurf
 M      CAT.glnx86/CAT_DumpCurv
 M      CAT.glnx86/CAT_DumpSurfArea
 M      CAT.glnx86/CAT_DumpSurfaceRatio
 M      CAT.glnx86/CAT_FixTopology
 M      CAT.glnx86/CAT_FractalDimension
 M      CAT.glnx86/CAT_Hausdorff
 M      CAT.glnx86/CAT_Isometize
 M      CAT.glnx86/CAT_MarkDefects
 M      CAT.glnx86/CAT_RefineMesh
 M      CAT.glnx86/CAT_ResampleSphericalSurf
 M      CAT.glnx86/CAT_ResampleSphericalSurfSPH
 M      CAT.glnx86/CAT_ResampleSurf
 M      CAT.glnx86/CAT_SelfIntersect
 M      CAT.glnx86/CAT_SeparatePolygon
 M      CAT.glnx86/CAT_SmoothConvexity
 M      CAT.glnx86/CAT_SulcusDepth
 M      CAT.glnx86/CAT_Surf2Sphere
 M      CAT.glnx86/CAT_Surf2Vol
 M      CAT.glnx86/CAT_SurfDistance
 M      CAT.glnx86/CAT_WarpSurf
MM      CAT.maca64/CAT_3dVol2Surf
MM      CAT.maca64/CAT_AddValuesToSurf
MM      CAT.maca64/CAT_AverageSurfaces
MM      CAT.maca64/CAT_BlurSurfHK
MM      CAT.maca64/CAT_Central2Pial
MM      CAT.maca64/CAT_DeformSurf
MM      CAT.maca64/CAT_DumpCurv
MM      CAT.maca64/CAT_DumpSurfArea
MM      CAT.maca64/CAT_DumpSurfaceRatio
MM      CAT.maca64/CAT_FixTopology
MM      CAT.maca64/CAT_FractalDimension
MM      CAT.maca64/CAT_Hausdorff
MM      CAT.maca64/CAT_Isometize
MM      CAT.maca64/CAT_MarkDefects
MM      CAT.maca64/CAT_RefineMesh
MM      CAT.maca64/CAT_ResampleSphericalSurf
MM      CAT.maca64/CAT_ResampleSphericalSurfSPH
MM      CAT.maca64/CAT_ResampleSurf
MM      CAT.maca64/CAT_SelfIntersect
MM      CAT.maca64/CAT_SeparatePolygon
MM      CAT.maca64/CAT_SmoothConvexity
MM      CAT.maca64/CAT_SulcusDepth
MM      CAT.maca64/CAT_Surf2Sphere
MM      CAT.maca64/CAT_Surf2Vol
MM      CAT.maca64/CAT_SurfDistance
MM      CAT.maca64/CAT_WarpSurf
 M      CAT.maci64/CAT_3dVol2Surf
 M      CAT.maci64/CAT_AddValuesToSurf
 M      CAT.maci64/CAT_AverageSurfaces
 M      CAT.maci64/CAT_BlurSurfHK
 M      CAT.maci64/CAT_Central2Pial
 M      CAT.maci64/CAT_DeformSurf
 M      CAT.maci64/CAT_DumpCurv
 M      CAT.maci64/CAT_DumpSurfArea
 M      CAT.maci64/CAT_DumpSurfaceRatio
 M      CAT.maci64/CAT_FixTopology
 M      CAT.maci64/CAT_FractalDimension
 M      CAT.maci64/CAT_Hausdorff
 M      CAT.maci64/CAT_Isometize
 M      CAT.maci64/CAT_MarkDefects
 M      CAT.maci64/CAT_RefineMesh
 M      CAT.maci64/CAT_ResampleSphericalSurf
 M      CAT.maci64/CAT_ResampleSphericalSurfSPH
 M      CAT.maci64/CAT_ResampleSurf
 M      CAT.maci64/CAT_SelfIntersect
 M      CAT.maci64/CAT_SeparatePolygon
 M      CAT.maci64/CAT_SmoothConvexity
 M      CAT.maci64/CAT_SulcusDepth
 M      CAT.maci64/CAT_Surf2Sphere
 M      CAT.maci64/CAT_Surf2Vol
 M      CAT.maci64/CAT_SurfDistance
 M      CAT.maci64/CAT_WarpSurf
 M      CAT.w32/CAT_3dVol2Surf.exe
 M      CAT.w32/CAT_AddValuesToSurf.exe
 M      CAT.w32/CAT_AverageSurfaces.exe
 M      CAT.w32/CAT_BlurSurfHK.exe
 M      CAT.w32/CAT_Central2Pial.exe
 M      CAT.w32/CAT_DeformSurf.exe
 M      CAT.w32/CAT_DumpCurv.exe
 M      CAT.w32/CAT_DumpSurfArea.exe
 M      CAT.w32/CAT_DumpSurfaceRatio.exe
 M      CAT.w32/CAT_FixTopology.exe
 M      CAT.w32/CAT_FractalDimension.exe
 M      CAT.w32/CAT_Hausdorff.exe
 M      CAT.w32/CAT_Isometize.exe
 M      CAT.w32/CAT_MarkDefects.exe
 M      CAT.w32/CAT_RefineMesh.exe
 M      CAT.w32/CAT_ResampleSphericalSurf.exe
 M      CAT.w32/CAT_ResampleSphericalSurfSPH.exe
 M      CAT.w32/CAT_ResampleSurf.exe
 M      CAT.w32/CAT_SelfIntersect.exe
 M      CAT.w32/CAT_SeparatePolygon.exe
 M      CAT.w32/CAT_SmoothConvexity.exe
 M      CAT.w32/CAT_SulcusDepth.exe
 M      CAT.w32/CAT_Surf2Sphere.exe
 M      CAT.w32/CAT_Surf2Vol.exe
 M      CAT.w32/CAT_SurfDistance.exe
 M      CAT.w32/CAT_WarpSurf.exe
M       CHANGES.txt
M       Contents.m
M       cat_conf_tools.m
M       cat_long_main.m
M       cat_surf_render2.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Fixed:   Corrected recognition of ROI use in tbx_cfg_cat.m
(2) Fixed:   Corrected use of original labelmaps in cat_surf_render2.m.
(3) Fixed:   Corrected YTickLabels in cat_surf_render2.m for annot files.
(4) Fixed:   Corrected deletion of temporary files in longitudinal pipeline.


------------------------------------------------------------------------
r1888 | gaser | 2021-10-12 15:49:25 +0200 (Tue, 12 Oct 2021) | 31 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_check_system_output.m
M       cat_conf_stools.m
M       cat_io_FreeSurfer.m
M       cat_long_multi_run.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_LAS.m
M       cat_main_LAS2.m
M       cat_main_reportfig.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_surf_createCS2.m
M       cat_surf_results.m
M       html/cat.html
M       spm_cat12.m

(1) Changed: Added call to sudo command from spm_cat12 if execution issues for
             mac systems occur due to Apple gatekeeper.
(2) Changed: Slightly changed values fpr volume to surface mapping to ensure
             that all values are considered in the cortex.
(3) Changed: Reformatedd cat_io_Freesurfer and added one more file check.
(4) Fixed:   Parameter "Affine" was sometimes not created in cat_run_job1639.m.
(5) Fixed:   Added some more parameter checks to cat_main_reportfig.m.
(6) Fixed:   Corrected progress output in cat_main_LAS.m, cat_main_LAS2.m,
             cat_main.m and cat_main1639.m.
(7) Fixed:   Corrected handling of BIDS structure in longitudinal data.


------------------------------------------------------------------------
r1887 | gaser | 2021-10-08 11:59:30 +0200 (Fri, 08 Oct 2021) | 121 lines

Changed paths:
A       CAT.glnx86
A       CAT.glnx86/CAT_3dVol2Surf
A       CAT.glnx86/CAT_AddValuesToSurf
A       CAT.glnx86/CAT_AverageSurfaces
A       CAT.glnx86/CAT_BlurSurfHK
A       CAT.glnx86/CAT_Central2Pial
A       CAT.glnx86/CAT_DeformSurf
A       CAT.glnx86/CAT_DumpCurv
A       CAT.glnx86/CAT_DumpSurfArea
A       CAT.glnx86/CAT_DumpSurfaceRatio
A       CAT.glnx86/CAT_FixTopology
A       CAT.glnx86/CAT_FractalDimension
A       CAT.glnx86/CAT_Hausdorff
A       CAT.glnx86/CAT_Isometize
A       CAT.glnx86/CAT_MarkDefects
A       CAT.glnx86/CAT_RefineMesh
A       CAT.glnx86/CAT_ResampleSphericalSurf
A       CAT.glnx86/CAT_ResampleSphericalSurfSPH
A       CAT.glnx86/CAT_ResampleSurf
A       CAT.glnx86/CAT_SelfIntersect
A       CAT.glnx86/CAT_SeparatePolygon
A       CAT.glnx86/CAT_SmoothConvexity
A       CAT.glnx86/CAT_SulcusDepth
A       CAT.glnx86/CAT_Surf2Sphere
A       CAT.glnx86/CAT_Surf2Vol
A       CAT.glnx86/CAT_SurfDistance
A       CAT.glnx86/CAT_WarpSurf
A       CAT.maca64
A       CAT.maca64/CAT_3dVol2Surf
A       CAT.maca64/CAT_AddValuesToSurf
A       CAT.maca64/CAT_AverageSurfaces
A       CAT.maca64/CAT_BlurSurfHK
A       CAT.maca64/CAT_Central2Pial
A       CAT.maca64/CAT_DeformSurf
A       CAT.maca64/CAT_DumpCurv
A       CAT.maca64/CAT_DumpSurfArea
A       CAT.maca64/CAT_DumpSurfaceRatio
A       CAT.maca64/CAT_FixTopology
A       CAT.maca64/CAT_FractalDimension
A       CAT.maca64/CAT_Hausdorff
A       CAT.maca64/CAT_Isometize
A       CAT.maca64/CAT_MarkDefects
A       CAT.maca64/CAT_RefineMesh
A       CAT.maca64/CAT_ResampleSphericalSurf
A       CAT.maca64/CAT_ResampleSphericalSurfSPH
A       CAT.maca64/CAT_ResampleSurf
A       CAT.maca64/CAT_SelfIntersect
A       CAT.maca64/CAT_SeparatePolygon
A       CAT.maca64/CAT_SmoothConvexity
A       CAT.maca64/CAT_SulcusDepth
A       CAT.maca64/CAT_Surf2Sphere
A       CAT.maca64/CAT_Surf2Vol
A       CAT.maca64/CAT_SurfDistance
A       CAT.maca64/CAT_WarpSurf
A       CAT.maci64
A       CAT.maci64/CAT_3dVol2Surf
A       CAT.maci64/CAT_AddValuesToSurf
A       CAT.maci64/CAT_AverageSurfaces
A       CAT.maci64/CAT_BlurSurfHK
A       CAT.maci64/CAT_Central2Pial
A       CAT.maci64/CAT_DeformSurf
A       CAT.maci64/CAT_DumpCurv
A       CAT.maci64/CAT_DumpSurfArea
A       CAT.maci64/CAT_DumpSurfaceRatio
A       CAT.maci64/CAT_FixTopology
A       CAT.maci64/CAT_FractalDimension
A       CAT.maci64/CAT_Hausdorff
A       CAT.maci64/CAT_Isometize
A       CAT.maci64/CAT_MarkDefects
A       CAT.maci64/CAT_RefineMesh
A       CAT.maci64/CAT_ResampleSphericalSurf
A       CAT.maci64/CAT_ResampleSphericalSurfSPH
A       CAT.maci64/CAT_ResampleSurf
A       CAT.maci64/CAT_SelfIntersect
A       CAT.maci64/CAT_SeparatePolygon
A       CAT.maci64/CAT_SmoothConvexity
A       CAT.maci64/CAT_SulcusDepth
A       CAT.maci64/CAT_Surf2Sphere
A       CAT.maci64/CAT_Surf2Vol
A       CAT.maci64/CAT_SurfDistance
A       CAT.maci64/CAT_WarpSurf
A       CAT.w32
A       CAT.w32/CAT_3dVol2Surf.exe
A       CAT.w32/CAT_AddValuesToSurf.exe
A       CAT.w32/CAT_AverageSurfaces.exe
A       CAT.w32/CAT_BlurSurfHK.exe
A       CAT.w32/CAT_Central2Pial.exe
A       CAT.w32/CAT_DeformSurf.exe
A       CAT.w32/CAT_DumpCurv.exe
A       CAT.w32/CAT_DumpSurfArea.exe
A       CAT.w32/CAT_DumpSurfaceRatio.exe
A       CAT.w32/CAT_FixTopology.exe
A       CAT.w32/CAT_FractalDimension.exe
A       CAT.w32/CAT_Hausdorff.exe
A       CAT.w32/CAT_Isometize.exe
A       CAT.w32/CAT_MarkDefects.exe
A       CAT.w32/CAT_RefineMesh.exe
A       CAT.w32/CAT_ResampleSphericalSurf.exe
A       CAT.w32/CAT_ResampleSphericalSurfSPH.exe
A       CAT.w32/CAT_ResampleSurf.exe
A       CAT.w32/CAT_SelfIntersect.exe
A       CAT.w32/CAT_SeparatePolygon.exe
A       CAT.w32/CAT_SmoothConvexity.exe
A       CAT.w32/CAT_SulcusDepth.exe
A       CAT.w32/CAT_Surf2Sphere.exe
A       CAT.w32/CAT_Surf2Vol.exe
A       CAT.w32/CAT_SurfDistance.exe
A       CAT.w32/CAT_WarpSurf.exe
M       CHANGES.txt
M       Contents.m
MM      batches/cat12_postmortem.m
M       cat_system.m
M       html/cat.html
 M      html/cat_methods_postmortem.html
 M      html/images/cat_methods_downsampling.jpg
 M      html/images/cat_methods_postmortem.jpg

(1) Changed: Added support of new Apple Silicon processors to cat_system.m
             and added new binaries for surface tools.

------------------------------------------------------------------------
r1886 | gaser | 2021-10-07 16:55:42 +0200 (Thu, 07 Oct 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_io_rerun.m
M       cat_system.m
M       html/cat.html

(1) Changed: Added recognition of new Apple Silicon processors to cat_system.m
(2) Fixed:   Corrected bug in cat_vol_sanlm/cat_io_rerun that always skipped
             SANLM filter in the last r1885 version.

------------------------------------------------------------------------
r1885 | dahnke | 2021-10-05 12:14:25 +0200 (Tue, 05 Oct 2021) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_stat_getCSVXMLfield.m
M       cat_stat_spm2x.m
M       cat_surf_parameters.m
M       cat_surf_resamp.m
M       cat_surf_surf2roi.m

(1) Fixed:    Corrected bugs in CSV/XML batch defintion and processing
              (cat_conf_tools & cat_stat_getCSVXMLfield).
(2) Fixed:    Corrected batch dependency bug cat_stat_spm2x.m
(3) Fixed:    Corrected bugs in area & lGI dependencies in cat_surf_parameters.
(4) Fixed:    Corrected bugs in cat_surf_resamp.
(5) Fixed:    Corrected export problems of special cases in cat_surf_surf2roi.


------------------------------------------------------------------------
r1884 | dahnke | 2021-10-04 13:27:03 +0200 (Mon, 04 Oct 2021) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_main1639.m
M       cat_vol_resize.m

(1) Fixed:      Corrected bug with uint8 data in cat_vol_resize and resize batch.
(2) Fixed:      Corrected calls of cat_main_gintnorm in cat_main1639.


------------------------------------------------------------------------
r1883 | dahnke | 2021-10-01 15:02:31 +0200 (Fri, 01 Oct 2021) | 83 lines

Changed paths:
M       CHANGES.txt
A       batches/cat12_postmortem.m
M       cat_conf_opts.m
M       cat_conf_tools.m
M       cat_io_rerun.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_clean_gwc.m
M       cat_main_gintnorm.m
M       cat_main_registration.m
M       cat_main_reportcmd.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_run_newcatch.m
M       cat_stat_marks.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_create_TPM_hull_surface.m
M       cat_surf_fun.m
M       cat_vol_headtrimming.m
M       cat_vol_morph.m
M       cat_vol_qa.m
M       cat_vol_resize.m
M       cat_vol_sanlm.m
M       html/cat.html
M       html/cat_methods.html
A       html/cat_methods_postmortem.html
A       html/images/cat_methods_downsampling.jpg
A       html/images/cat_methods_postmortem.jpg
M       templates_animals_surfaces/bh.headbrain.chimpanzee_TPM.gii

This update focuses on corrections for the processing of post-mortem/skull-stripped
PD-weighted ultra-high-resolution data for the SPM and CAT preprocessing.
(1) Changed:  Extended cat_main_clean_cgw to support input files rather than
              the 4D tissue matrix (changes also in cat_main[1639]). Added new
              parameter for additional cleanup, e.g. in PD/T2 (post-mortem) data.
              Added resolution depending definition that is defined by matrix size
              to keep it simple.
(2) Fixed:    Only run SPM pipeline if c1 files are selected (cat_run_job[1639]).
(3) Fixed:    Corrected CAT report output in case of SPM input segmentation, i.e.,
              display SPM Segmentation parameter (cat_main_report[str/fig]).
(4) Changed:  Added auto option to create resolution-specific prefixes in
              cat_vol_resize and cat_conf_tools.
(5) Changed:  Increased number of iterations to stronger reduce self-intersections
              in severe cases.
(6) Fixed:    Corrected settings for ex-vivo PD/T2 processing in cat_main_gintnorm
              but not cat_main_gintnorm1639 (default T1 pipeline).
(7) Fixed:    Added handling of INF boundary box setting in cat_main_registration.
(8) Fixed:    Extended iterations in case of high amount of self-intersections in
              sub-function cat_surf_collision_correction_[pbt|ry]. Added output of
              reminding percent of self-intersections.
(9) Fixed:    Corrected use of expert parameters.
(10) New:     Added lazy parameter to denoising and trimming batch
              (cat_vol_sanlm, cat_vol_headtrimming, cat_conf_tools)
(11) Fixed:   Corrected handling of post-mortem / skull-stripped SPM segmentation
              with 3 and 4 classes in cat_run_job[1639].
(12) Fixed:   Corrected vx_vol dependency for matrix enlargement of opening
              operations in cat_vol_morph (only relevant for resolution <0.5mm).
(13) Fixed:   Corrected a bug in cat_io_rerun and extended the test output (verb=1).
(14) New:     Added HTML help page cat_methods_postmortem and two images.
(15) Changed: Multiple small changes in cat_main[1639] for very special cases:
              - Updated call of global normalization for ultra-high-resolution data.
              - Updated call of cleanup for ultra-high-resolution data.
              - Corrected order of processed surface.
              - Added Ycls Updates to cat_main_SPMpp.
(16) Change:  Updated handling of post-mortem and ultra-high-resolution data in
              cat_main_updateSPM[1639].m.
(17) Fixed:   Extend limitation of mark2grad @function in cat_run, cat_stat_marks,
              and cat_main_reportstr.
(18) Fixed:   Corrected problems in different global thickness values (PBT vs. FS)
              in cat_surf_createCS[2].
(19) Changed: Corrected definition of brain/head average surface for CAT report in
              cat_surf_create_TPM_hull_surface
(20) Fixed:   Corrected incorrect use of exist in surface render in cat_main_reportfig.
(21) New:     Added post-mortem batch batch/cat12_postmortem.m


------------------------------------------------------------------------
r1882 | gaser | 2021-09-30 12:24:45 +0200 (Thu, 30 Sep 2021) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_run_job_APRGs.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_results.m
M       templates_MNI152NLin2009cAsym/aal3.csv

(1) Changed: Added some new command line options to cat_surf_results.m and also
             implemented a new flat design for ROI display.
(2) Changed: Added option for new flat design for ROI display to
             cat_stat_analyze_ROIs.m
(3) Fixed:   Corrected label for rIFGoperc which was doubled (value 6). Thanks
             to Peter Mondrup Rasmussen for pointing to that.


------------------------------------------------------------------------
r1881 | gaser | 2021-09-29 16:09:02 +0200 (Wed, 29 Sep 2021) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_tools.m
M       cat_run_job_APRGs.m
M       cat_run_newcatch.m
M       html/cat.html

(1) Changed: Updated error output for piwik to better indicated CAT release
             number.
(2) Fixed:   Use try/catch to also consider older versions of spm_maff8.m from
             previous SPM12 updates.


------------------------------------------------------------------------
r1880 | gaser | 2021-09-28 14:04:36 +0200 (Tue, 28 Sep 2021) | 27 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_factorial.m
M       cat_install_atlases.m
M       cat_main_reportfig.m
M       cat_spm_results_ui.m
M       cat_stat_marks.m
M       cat_surf_createCS2.m
M       html/cat.html

(1) Changed: Re-structured cat_io_senderrormail.m and removed sending of zipped
             err-folder which was almost never used. Now the content of the
             resp. xml-file and optionally the log-file will be sended and will
             be opened in editor.
(2) Changed: Updated description of quality measures in help text.
(3) Changed: Added automatical installation of CAT12 to cat_spm_results_ui.m.
(4) Changed: Moved "Quick Start Guide" to own button in GUI.
(5) Fixed:   Corrected error in cat_surf_createCS2.m that occurred using fast
             surface extraction.
(6) Fixed:   Corrected check for existence of hSD variable and again added more
             try commands to catch mysterious errors o windows systems in
             cat_surf_createCS2.m
(7) Fixed:   Updated cat_install_atlases to correctly find ROI names.


------------------------------------------------------------------------
r1879 | gaser | 2021-09-03 10:24:31 +0200 (Fri, 03 Sep 2021) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       cat_main_reportfig.m
M       cat_main_roi.m
M       cat_run_job1639.m
M       html/cat.html

(1) Fixed: Added check that affine transformation was successfully saved in
           in xml-file for use of priors in longitudinal pipeline.
(2) Fixed: Added check that index to FA variable is correct in cat_main_roi.m.
(3) Fixed: Again added new checks that some variables exist in
           cat_main_reportfig.m.
(4) Fixed: Added check that intensity update in cat_main.m was successful.

------------------------------------------------------------------------
r1878 | gaser | 2021-09-01 16:37:14 +0200 (Wed, 01 Sep 2021) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_long_multi_run.m

Fixed: Removed wrong indexing in cat_long_multi_run.m

------------------------------------------------------------------------
r1877 | gaser | 2021-09-01 16:23:58 +0200 (Wed, 01 Sep 2021) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_long_multi_run.m

Fixed: Removed debugging code from cat_long_multi_run.m

------------------------------------------------------------------------
r1876 | gaser | 2021-09-01 16:08:49 +0200 (Wed, 01 Sep 2021) | 19 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_long.m
M       cat_io_subfolders.m
M       cat_long_multi_run.m
M       cat_main_reportfig.m
M       cat_run.m
M       cat_stat_check_cov.m
M       cat_surf_createCS2.m
M       html/cat.html

(1) Changed: Added BIDS support and support for nii.gz files to longitudinal
             pipeline.
(2) Fixed:   Corrected bug in cat_stat_check_cov.m that were caused if surface
             measures in report file were not availble.
(3) Fixed:   Added one more try/catch to cat_main_reportfig.m to prevent errors
             on windows systems.

------------------------------------------------------------------------
r1875 | gaser | 2021-08-27 10:25:20 +0200 (Fri, 27 Aug 2021) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_check_cov.m
M       cat_surf_createCS2.m
M       cat_surf_surf2roi.m
M       cat_vol_series_align.m
M       html/cat.html

(1) Fixed: Again corrected BIDS handling in cat_surf_surf2roi.m and
           cat_surf_createCS2.m.
(2) Fixed: Corrected number of xml-files in cat_stat_check_cov.m.

------------------------------------------------------------------------
r1874 | gaser | 2021-08-26 11:00:39 +0200 (Thu, 26 Aug 2021) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
MM      cat_io_load.m
M       cat_run_job1639.m
M       html/cat.html

Fixed: Corrected bug in writing catlog file.

------------------------------------------------------------------------
r1873 | gaser | 2021-08-26 08:58:44 +0200 (Thu, 26 Aug 2021) | 18 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_io_handle_pre.m
M       cat_io_subfolders.m
M       cat_main1639.m
M       cat_main_reportfig.m
M       cat_run_newcatch.m
M       cat_surf_createCS2.m
M       cat_surf_surf2roi.m
M       cat_vol_qa.m
M       html/cat.html

(1) Changed: Tried to remove annoying warning with spm_orthviews under Windows
             systems.
(2) Changed: Added errfolder to cat_io_subfolder.m.
(3) Fixed:   Corrected writing of BIDS structure.

------------------------------------------------------------------------
r1872 | gaser | 2021-08-20 17:52:58 +0200 (Fri, 20 Aug 2021) | 17 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
A       cat_io_load.m
M       cat_main_reportfig.m
M       cat_run_job1639.m
M       cat_stat_analyze_ROIs.m
M       html/cat.html

(1) Changed: Added message to cat_stat_analyze_ROIs.m if no results were found
             (also for correction for multiple comparisons).
(2) Fixed:   Added additional check if log-file was not deleted during
             preprocessing in cat_run_job1639.m.
(3) Fixed:   Added more try/catch commands to cat_main_reportfig.m because
             of unclear crashes.


------------------------------------------------------------------------
r1871 | dahnke | 2021-08-03 17:03:02 +0200 (Tue, 03 Aug 2021) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS2.m

(1) Fixed:    Corrected bug and debugging setting in cat_surf_createCS.

------------------------------------------------------------------------
r1870 | dahnke | 2021-08-02 16:41:36 +0200 (Mon, 02 Aug 2021) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_surf_createCS2.m

(1) Changed:   Set parahippocampal gyrus closing as default.
(2) Changed:   Deactivated local smoothing of problematic surface
               structures (need further tests).

------------------------------------------------------------------------
r1869 | dahnke | 2021-07-29 21:57:52 +0200 (Thu, 29 Jul 2021) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS2.m
M       cat_surf_fun.m
M       cat_vol_qa.m

(1) Fixed:    Corrected a bug in the local smoothing of the ICR estimation that
              result in severe overstimation in noisy data because the masking
              was not working correctly.
(2) Fixed:    Corrected bug with internal/missing function by public one in
              cat_surf_createCS2 and cat_surf_fun.


------------------------------------------------------------------------
r1868 | dahnke | 2021-07-29 17:21:21 +0200 (Thu, 29 Jul 2021) | 24 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_main_update_intnorm.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m

(1) Fixed:   Corrected problems with CSF holes in the reconstruction of the
             parahippocampal gyrus in the default surface creation pipeline
             in cat_surf_createCS. Added subfunction for local surface smoothing
             in cat_surf_fun.
(2) Fixed:   Corrected small bugs in cat_conf_tools and cat_vol_headtrimming.
(3) Changed: Debugging blocks in cat_main1639 to test surface reconstruction.
(4) Changed: Added new skull-stripping mode for post-mortem data with CSF=BG
             that need 3 rather than 4 classes with changes in cat_conf_extopts
             and cat_run_job[1639], cat_main[1639].

------------------------------------------------------------------------
r1867 | gaser | 2021-07-27 13:22:08 +0200 (Tue, 27 Jul 2021) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main_amap.m
M       cat_run_job.m
M       cat_stat_quality_measures.m
M       html/cat.html
M       spm_cat12.m

(1) Changed: Replaced volume reading functions in cat_stat_quality_measures.m
             by faster nifti functions.
(2) Fixed:   Corrected bugs in backup pipeline.


------------------------------------------------------------------------
r1866 | dahnke | 2021-07-27 09:29:56 +0200 (Tue, 27 Jul 2021) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_main1639.m
M       cat_surf_createCS2.m
M       cat_vol_headtrimming.m

(1) Fixed:   Corrected problems with CSF holes in the reconstruction of the
             parahippocampal gyrus in the default surface creation pipeline
             in cat_surf_createCS.
(2) Fixed:   Corrected small bugs in cat_conf_tools and cat_vol_headtrimming.
(3) Changed: Debugging blocks in cat_main1639 to test surface reconstruction.


------------------------------------------------------------------------
r1865 | dahnke | 2021-07-24 13:06:23 +0200 (Sat, 24 Jul 2021) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_getCSVXMLfield.m
M       cat_surf_createCS2.m
M       cat_vol_resize.m

(1) Fixed:   Corrected problems in the reconstruction of the parahippocampal gyrus
             in the default surface creation pipeline with downsampled volumes in
             cat_surf_createCS2.
(2) Changed: Added smoothing option to for low-resolution resampling of the surface
             map (used to control the number of vertices) in cat_vol_resize.
(3) Changed: Added recoding setting to code variables (eg. scan site) in
             cat_stat_getCSVXMLfields.


------------------------------------------------------------------------
r1864 | dahnke | 2021-07-20 16:41:40 +0200 (Tue, 20 Jul 2021) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_ROI.m
M       cat_main1639.m
M       cat_main_LAS2.m
M       cat_main_reportstr.m
M       cat_run.m
M       cat_surf_createCS2.m
M       cat_vol_resize.m

(1) Changed:  Small cosmetic changes in cat_conf_ROI.
(2) Fixed:    Corrected filling of parahippocampal wholes in cat_surf_createCS
              and cat_main[1639] if extopts.close_parahipp is activated.
(3) Fixed:    Added try-catch block in cat_main_LAS2.m to avoid error in
              SPM pipeline data.

------------------------------------------------------------------------
r1863 | dahnke | 2021-07-20 16:19:57 +0200 (Tue, 20 Jul 2021) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_main1639.m
M       cat_spm_results_ui.m
M       cat_stat_check_cov.m
M       cat_stat_getCSVXMLfield.m
M       cat_surf_createCS2.m

(1) Fixed:   Corrected surface ROI processing time output in cat_main1639.
(2) Fixed:   Corrected bugs in XML/CSV extraction batch and added fields to extract
             data from filename in cat_conf_tools and cat_stat_getCSVXMLfield.
(3) Fixed:   Corrected bug in contrast definition in cat_spm_results_ui.
(4) Fixed:   Corrected tiny bug in cat_stat_check_cov.
(5) Fixed:   Catche bug in surface defect output in cat_surf_createCS2
             that has to be corrected another time.


------------------------------------------------------------------------
r1862 | gaser | 2021-07-20 09:23:43 +0200 (Tue, 20 Jul 2021) | 16 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_stat_check_cov.m
M       cat_stat_quality_measures.m

(1) Changed: Speed up calculation of SD and z-score in
             cat_stat_quality_measures.m
(2) Changed: Added further check that xml-files exist in cat_stat_check_cov.m
             and cat_stat_quality_measures.m.
(3) Changed: Updated help text for sample homogeneity check.
(4) Changed: Changed version in Makefile to CAT12.8.


------------------------------------------------------------------------
r1861 | gaser | 2021-07-13 09:43:37 +0200 (Tue, 13 Jul 2021) | 20 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_main_reportfig.m
M       cat_stat_check_cov.m
M       cat_stat_confplot_spm.m
M       cat_stat_quality_measures.m
M       cat_surf_resamp.m
M       html/cat.html

(1) Changed: Added some more try/catch commands to cat_main_reportfig.m to
             handle unexpected errors that some times caused.
(2) Changed: Simplified file handling in cat_stat_quality_measures.m.
(3) Changed: Removed option to send error messages from CAT12 GUI because this
             is now handled automatically.
(4) Fixed:   Corrected handling of rigid or affine transformed data in
             cat_stat_check_cov.m and cat_stat_quality_measures.m.


------------------------------------------------------------------------
r1860 | gaser | 2021-07-11 21:53:45 +0200 (Sun, 11 Jul 2021) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_io_senderrormail.m
M       cat_run.m
M       cat_run_newcatch.m

(1) Changed: Re-structured cat_io_senderrormail.m and removed sending of zipped
             err-folder which was almost never used. Now the content of the
             resp. xml-file and optionally the log-file will be sended and will
             be opened in editor.
(2) Changed: Added creation of mail report if errors occur in cat_run_newcatch.m
             and cat_run.m.


------------------------------------------------------------------------
r1859 | dahnke | 2021-07-09 16:08:57 +0200 (Fri, 09 Jul 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main1639.m
M       cat_main_roi.m

(1) Fixed:   Corrected bug in ROI export that removed the first
             region as header in cat_main_roi.
(2) Fixed:   Corrected unmeant deletion of FreeSurfer average files
             in case of preview surfaces in cat_main[1639].

------------------------------------------------------------------------
r1858 | dahnke | 2021-07-09 12:44:07 +0200 (Fri, 09 Jul 2021) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_tools.m
M       cat_stat_getCSVXMLfield.m

(1) Changed:  Updated configuration of XML/CSV batch in cat_conf_tools
              and cat_stat_getCSVXMLfield.

------------------------------------------------------------------------
r1857 | gaser | 2021-07-05 12:59:44 +0200 (Mon, 05 Jul 2021) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       html/cat.html

(1) Changed: Removed call to counter.html from cat12.m.
(1) Fixed:   Added *.freesurfer.gii files again to templates_surfaces


------------------------------------------------------------------------
r1856 | gaser | 2021-07-01 22:31:09 +0200 (Thu, 01 Jul 2021) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main_reportfig.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m
M       html/cat.html

(1) Fixed: Corrected bug in surface collission code in cat_surf_fun.m.
(2) Fixed: Added try/end code to cat_main_reportfig.m because sometimes creation
           of axes failed.

------------------------------------------------------------------------
r1855 | dahnke | 2021-07-01 15:56:52 +0200 (Thu, 01 Jul 2021) | 30 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_io_volctype.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_amap.m
M       cat_main_reportstr.m
M       cat_main_roi.m
M       cat_main_updateWMHs.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_surf_resamp.m
M       cat_vol_ctype.m
M       cat_vol_resize.m

(1) Changed: Improved error output in cat_run.
(2) Fixed:   Corrected bugs in resize batch (cat_vol_resize).
(3) Fixed:   Corrected bugs in CAT preprocessing with SPM input maps in
             in cat_run_job[1639], cat_main[1639], spm_main_reportstr, and
             cat_main_updateWMHs.
(4) Fixed:   Corrected problem in exporting own atlas ROIs in cat_main_roi.
(5) Fixed:   Corrected resize batch menu in cat_conf_tools.
(6) Fixed:   Corrected bugs in cat_vol_resize.
(7) Fixed:   Corrected bug in file handling in cat_surf_resamp.
(8) Fixed:   Corrected problems in cat_io_volctype.
(9) Changed: Specified segmentation mixing alert message in cat_main_amap.


------------------------------------------------------------------------
r1854 | gaser | 2021-06-30 12:21:50 +0200 (Wed, 30 Jun 2021) | 12 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_spm_results_ui.m
M       html/cat.html

(1) Changed: Updated CAT12 manual.
(2) Fixed:   Corrected path if results are called from another folder in
             cat_spm_results_ui.m.

------------------------------------------------------------------------
r1853 | gaser | 2021-06-29 14:24:57 +0200 (Tue, 29 Jun 2021) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_ROI.m
M       cat_conf_tools.m
M       html/cat.html
M       html/cat.txt
M       html/cat_versions.html

(1) Changed: Added interactive links to version information.
(2) Fixed:   Corrected links to atlases in html-files.
(3) Fixed:   Corrected braces for help text in cat_conf_tools.m.


------------------------------------------------------------------------
r1852 | gaser | 2021-06-28 23:47:22 +0200 (Mon, 28 Jun 2021) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_main1639.m
M       cat_main_registration.m
M       cat_main_reportfig.m
M       cat_run_job1639.m
M       cat_vol_slice_overlay.m
 M      templates_animals/chimpanzee_atlas_davi.csv
 M      templates_animals/chimpanzee_atlas_davi.txt

(1) Fixed: Added try/catch to cat_vol_slice_overlay.m to handle subfolders.
(2) Fixed: Added try/catch to ct_run_job1639.m to use older SPM12 versions.
(3) Fixed: Tried to remove some sources of errors in cat_main_reportfig.m.
(4) Fixed: Removed error in cat_main1639.m if SPM segmentation is used.

------------------------------------------------------------------------
r1851 | dahnke | 2021-06-28 14:44:14 +0200 (Mon, 28 Jun 2021) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_vol_resize.m

(1) Changed:  Corrected parameter definions and updated help in resize batch
              with changes in cat_conf_tools and cat_vol_resize.

------------------------------------------------------------------------
r1850 | dahnke | 2021-06-28 11:59:10 +0200 (Mon, 28 Jun 2021) | 52 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_registration.m
M       cat_main_roi.m
M       cat_main_updateSPM.m
M       cat_main_write.m
M       cat_run.m
M       cat_tst_calc_kappa.m
M       cat_tst_qa_cleaner.m
M       cat_vol_qa.m
M       cat_vol_resize.m
MM      cat_vol_sample.m
 M      html/images/cat_SLC_msk_c0009s0010t01A.png
M       internal/cat_tst_BWPres.m
M       templates_animals/chimpanzee_T1.nii
M       templates_animals/chimpanzee_TPM.nii
M       templates_animals/chimpanzee_Template_0_GS.nii
M       templates_animals/chimpanzee_Template_1_GS.nii
M       templates_animals/chimpanzee_Template_2_GS.nii
M       templates_animals/chimpanzee_Template_3_GS.nii
M       templates_animals/chimpanzee_Template_4_GS.nii
A       templates_animals/chimpanzee_atlas_davi.csv
M       templates_animals/chimpanzee_atlas_davi.nii
A       templates_animals/chimpanzee_atlas_davi.txt
M       templates_animals/chimpanzee_brainmask.nii
M       templates_animals/chimpanzee_cat.nii

(1) Changed:  Updated 1 mm chimpanzee template.
              See also http://junachimp.inm7.de/
(2) Changed:  Added full data export in cat_main_registration and cat_main_write
              in case of multiple ouput resolutions (extopts.vox) and experimental
              setting (extopts.experimental) in the developer mode to support
              evaluation of enhanced Shooting templates (also include changes
              in cat_main[1639].
(3) Fixed:    Corrected tiny bug with extended vox value in cat_main_roi.
(4) New:      Added new cases in the image resolution batch to reduce images
              with denoising by smoothing within the reduced neighborhood in
              cat_conf_tools and cat_vol_resize.
(5) Fixed:    Corrected problems in cat_vol_qa in case of other missig bias
              corrected map and added some missed variables.
(6) Fixed!:   Added missed log scaling in noise estimation that compensates the
              variing amount of voxels that are averaged in the resolution
              reduction! This reduces the underestimation of noise in high-res
              images. It also reduces noise overestimations in low resolution
              data but these are less obvious in IQR because of generally worse
              resolution rating in such images.
(7) Changed:  Tiny cosmetic changes in cat_tst_qa_cleaner and cat_tst_calc_kappa.


------------------------------------------------------------------------
r1849 | dahnke | 2021-06-25 11:05:24 +0200 (Fri, 25 Jun 2021) | 32 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_io_addwarning.m
M       cat_main1639.m
M       cat_main_registration.m
M       cat_main_reportcmd.m
M       cat_main_write.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_surf_fun.m
MM      internal/cat_vol_gbdist.m
 M      templates_animals_surfaces/bh.headbrain.ape_greater_TPM.gii
 M      templates_animals_surfaces/bh.headbrain.chimpanzee_TPM.gii
 M      templates_animals_surfaces/bh.headbrain.monkey_oldworld_TPM.gii
 M      templates_surfaces/mesh.inflated.freesurfer.gii
 M      templates_surfaces_32k/mesh.inflated.freesurfer.gii

(1) Fixed:   Corrected typos in cat_run, cat_main_write, cat_main_reportcmd.
(2) Fixed:   Corrected bugs in cat_main_registration in Dartel and backup
             pipeline.
(3) Fixed:   Corrected imat-error in cat_surf_fun.
(4) Changed: Use warning/alert rather than error in case of (very) low
             resolutions in cat_run_job[1639].
(5) Changed: Added real warning and error in cat_io_warning.
(6) New:     Added batch to call the image quality estimation for own
             input data with given segmentation in cat_conf_tools.
             Called function cat_vol_qa is currently not ready and the
             batch is only visible for developer.


------------------------------------------------------------------------
r1848 | gaser | 2021-06-05 23:51:45 +0200 (Sat, 05 Jun 2021) | 6 lines

Changed paths:
M       CHANGES.txt
R       cat_vol_sample.m

Changed: Added cat_vol_sample.m again.

------------------------------------------------------------------------
r1847 | dahnke | 2021-06-05 12:59:59 +0200 (Sat, 05 Jun 2021) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_io_colormaps.m
M       cat_main_reportcmd.m
M       cat_run.m
M       html/cat_methods_VBM.html
A       html/images/cat_SLC_msk_c0009s0010t01A.png

(1) Changed: Added Stroke Lesion Correction (SLC) HTML help page.
(2) Changed: Improved CAT preprocessing progress report in cat_main_reportcmd
             and cat_run.
(3) Changed: Updated comments in cat_io_colormap.


------------------------------------------------------------------------
r1846 | dahnke | 2021-06-03 16:41:00 +0200 (Thu, 03 Jun 2021) | 27 lines

Changed paths:
M       CHANGES.txt
M       cat_main_gintnorm.m
M       cat_main_reportfig.m
M       cat_surf_create_TPM_hull_surface.m
A       internal/cat_vol_gbdist.m
A  +    templates_animals_surfaces/bh.headbrain.ape_greater_TPM.gii
        > moved from templates_surfaces/bh.headbrain.ape_greater_TPM.gii
A  +    templates_animals_surfaces/bh.headbrain.chimpanzee_TPM.gii
        > moved from templates_surfaces/bh.headbrain.chimpanzee_TPM.gii
A  +    templates_animals_surfaces/bh.headbrain.monkey_oldworld_TPM.gii
        > moved from templates_surfaces/bh.headbrain.monkey_oldworld_TPM.gii
D       templates_surfaces/bh.headbrain.ape_greater_TPM.gii
        > moved to templates_animals_surfaces/bh.headbrain.ape_greater_TPM.gii
D       templates_surfaces/bh.headbrain.chimpanzee_TPM.gii
        > moved to templates_animals_surfaces/bh.headbrain.chimpanzee_TPM.gii
D       templates_surfaces/bh.headbrain.monkey_oldworld_TPM.gii
        > moved to templates_animals_surfaces/bh.headbrain.monkey_oldworld_TPM.gii

(1) Changed: Moved animal TPM template surface to animal directory and corrected
             handling in cat_main_reportfig and cat_surf_create_TPM_hull_surface.
(2) Changed: Corrected tiny bug in cat_main_gintnorm.
(3) New:     Added alternative voxel-based distance function cat_vol_gbdist that
             estimated the distance to a isosurface of a volume by using a graph-
             based nearest neighbor search, allow also to consider PVE values.


------------------------------------------------------------------------
r1845 | dahnke | 2021-06-03 14:29:43 +0200 (Thu, 03 Jun 2021) | 16 lines

Changed paths:
M       CHANGES.txt
A       cat_vol_sample.m
D       internal/cat_admin_create_estwrite_version.m
D       internal/old
A       templates_surfaces/bh.headbrain.ape_greater_TPM.gii
A       templates_surfaces/bh.headbrain.chimpanzee_TPM.gii
A       templates_surfaces/bh.headbrain.monkey_oldworld_TPM.gii
A       templates_surfaces/mesh.inflated.freesurfer.gii
A       templates_surfaces_32k/mesh.inflated.freesurfer.gii

(1) Deleted:  Removed old unused internal functions.
(2) New:      Added some general surfaces.
(3) New:      Added missing? cat_vol_sample function.


------------------------------------------------------------------------
r1844 | gaser | 2021-06-03 01:40:58 +0200 (Thu, 03 Jun 2021) | 18 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_factorial.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_stat_check_cov.m
M       check_pipeline_homogeneity.m
M       html/cat.html

(1) Changed: Added option for release check to check_pipeline_homogeneity.m.
(2) Changed: New median mapping function for mapping volume data to surface.
(3) Changed: Recompiled surface code.
(3) Fixed:   Corrected check for size check between xml-files and data in
             cat_stat_check_cov.m.
(4) Fixed:   Corrected estimation of mean values for dummy covariate in
             cat_conf_factorial.m.

------------------------------------------------------------------------
r1843 | dahnke | 2021-06-02 18:24:44 +0200 (Wed, 02 Jun 2021) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main1639.m
D       cat_main_LAS21639.m
D       cat_main_registration2.m
M       cat_surf_vx2surf.m

(1) Fixed:   Added missed variable in cat_main if it is called from cat_run_job1639.
(2) Fixed:   Correct typo in cat_surf_vx2surf.m.
(3) Deleted: Removed obsolete cat_main_LAS21639 (with old comment in cat_main1639)
             and cat_main_registration2.


------------------------------------------------------------------------
r1842 | gaser | 2021-06-01 16:41:58 +0200 (Tue, 01 Jun 2021) | 35 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_conf_extopts.m
M       cat_conf_opts.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_io_report.m
M       cat_long_biascorr.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_APRG.m
M       cat_main_LAS.m
M       cat_main_LAS2.m
M       cat_main_LAS21639.m
M       cat_main_LASs.m
M       cat_main_amap1639.m
M       cat_main_correctmyelination.m
M       cat_main_roi.m
M       cat_parallelize.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_epivolsurf.m
M       cat_surf_fun.m
M       cat_vol_partvol.m
M       cat_vol_partvol1639.m
M       cat_vol_sanlm.m
M       development/cat_main_LAS.m
M       html/cat_methods_validation.html
M       standalone/cat_standalone_segment.m
M       standalone/cat_standalone_segment_enigma.m
M       standalone/cat_standalone_segment_long.m

Changed: Corrected consistent typo in many files.

------------------------------------------------------------------------
r1841 | gaser | 2021-06-01 12:03:38 +0200 (Tue, 01 Jun 2021) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat12.m
M       cat_run.m
M       html/cat.html
M       standalone/cat_standalone.sh
MM      standalone/cat_standalone_get_ROI_values.m
MM      standalone/cat_standalone_segment_enigma.m

(1) Changed: Added BIDS writing to subfolder that is named by cat12 version for
             cat_standalone_segment_enigma.m.
(2) Changed: Some small edits to help text.
(3) Changed: Updated scp for deployed versions in Makefile.

------------------------------------------------------------------------
r1840 | dahnke | 2021-06-01 09:02:08 +0200 (Tue, 01 Jun 2021) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_main_LASs.m
M       cat_main_gintnorm.m
M       cat_run.m

(1) Fixed:   Corrected small bugs in cat_main_LASs, which is used exclusively
             by non-T1 weighted images in cat_main.
(2) Fixed:   Use kmeans instead of median in cat_main_gintnorm, which is used
             exclusively by cat_main.
(3) Fixed:   Corrected problems in progress report and conclusion in cat_run.


------------------------------------------------------------------------
r1839 | gaser | 2021-05-31 16:09:32 +0200 (Mon, 31 May 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_run_job1639.m
M       html/cat.html

(1) Changed: Updated Makefile part for scp of precompiled version.
(2) Fixed:   Removed some changes from r1834 in cat_run_job1639.m that caused
             issues for longitudinal data.

------------------------------------------------------------------------
r1838 | gaser | 2021-05-30 22:56:34 +0200 (Sun, 30 May 2021) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_ROI.m
M       cat_conf_tools.m
M       standalone/cat_standalone.sh
A       standalone/cat_standalone_get_ROI_values.m

(1) Added:   Added new standalone batch script for saving ROI values.
(2) Changed  Updated help text for cat_standalone.sh.



------------------------------------------------------------------------
r1837 | gaser | 2021-05-30 02:42:09 +0200 (Sun, 30 May 2021) | 51 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
MM      cat_stat_quality_measures.m
M       standalone/cat_standalone.sh
A  +    standalone/cat_standalone_deface.m
        > moved from standalone/cat_standalone_deface.txt
D       standalone/cat_standalone_deface.txt
        > moved to standalone/cat_standalone_deface.m
A  +    standalone/cat_standalone_dicom2nii.m
        > moved from standalone/cat_standalone_dicom2nii.txt
D       standalone/cat_standalone_dicom2nii.txt
        > moved to standalone/cat_standalone_dicom2nii.m
A  +    standalone/cat_standalone_get_quality.m
        > moved from standalone/cat_standalone_get_quality.txt
D       standalone/cat_standalone_get_quality.txt
        > moved to standalone/cat_standalone_get_quality.m
A  +    standalone/cat_standalone_resample.m
        > moved from standalone/cat_standalone_resample.txt
D       standalone/cat_standalone_resample.txt
        > moved to standalone/cat_standalone_resample.m
A  +    standalone/cat_standalone_segment.m
        > moved from standalone/cat_standalone_segment.txt
D       standalone/cat_standalone_segment.txt
        > moved to standalone/cat_standalone_segment.m
A       standalone/cat_standalone_segment_enigma.m
A  +    standalone/cat_standalone_segment_long.m
        > moved from standalone/cat_standalone_segment_long.txt
D       standalone/cat_standalone_segment_long.txt
        > moved to standalone/cat_standalone_segment_long.m
A  +    standalone/cat_standalone_simple.m
        > moved from standalone/cat_standalone_simple.txt
D       standalone/cat_standalone_simple.txt
        > moved to standalone/cat_standalone_simple.m
A  +    standalone/cat_standalone_smooth.m
        > moved from standalone/cat_standalone_smooth.txt
D       standalone/cat_standalone_smooth.txt
        > moved to standalone/cat_standalone_smooth.m
A  +    standalone/cat_standalone_tfce.m
        > moved from standalone/cat_standalone_tfce.txt
D       standalone/cat_standalone_tfce.txt
        > moved to standalone/cat_standalone_tfce.m

(1) Changed: Renamed standalone txt scripts to matlab files for easier use as
             common batch file.
(2) Changed: Updated help text for cat_standalone.sh.
(3) Fixed:   Corrected parameters in cat_standalone_get_quality.m
(4) Fixed:   Corrected call of quality saving tool in cat12.m.
(5) Added:   Added new standalone batch script for segmentation of Enigma data
             that also includes defacing.

------------------------------------------------------------------------
r1836 | gaser | 2021-05-29 01:21:13 +0200 (Sat, 29 May 2021) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_main_updateSPM.m
M       cat_run_job1639.m

Changed: Some smaller changes in formatting.

------------------------------------------------------------------------
r1835 | gaser | 2021-05-29 01:07:21 +0200 (Sat, 29 May 2021) | 25 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat12.m
M       cat_conf_tools.m
M       cat_stat_IQR.m
M       cat_stat_check_cov.m
M       cat_stat_check_cov2.m
A       cat_stat_quality_measures.m
M       html/cat_methods_QA.html
M       html/cat_versions.html
M       standalone/cat_standalone.sh
A       standalone/cat_standalone_get_quality.txt
 M      templates_MNI152NLin2009cAsym/thalamus.csv
 M      templates_MNI152NLin2009cAsym/thalamus.nii
MM      templates_MNI152NLin2009cAsym/thalamus.txt
 M      templates_external/MNI152NLin2009cSym.nii
 M      templates_external/y_MNI152NLin2009cSym_to_MNI152NLin2009cAsym.nii

(1) Added:   New function to estimate and save quality measures for external
             analysis.
(2) Added:   New standalone tool for abovementioned function.
(3) Changed: Added automatically search for xml-files for cat_stat_check_cov.m.
(4) Changed: Updated CAT12 manual and version information.

------------------------------------------------------------------------
r1834 | dahnke | 2021-05-28 16:45:20 +0200 (Fri, 28 May 2021) | 39 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main1639.m
M       cat_main_LASs.m
M       cat_main_amap.m
M       cat_main_gintnorm.m
M       cat_main_gintnormi.m
M       cat_main_registration.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_surf_fun.m
M       cat_surf_render2.m
M       cat_vol_iscaling.m
M       cat_vol_partvol.m
M       cat_vol_qa.m
M       cat_vol_sanlm.m

(1) Fixed:   Tested the new cat_main pipeline in case of non-T1 contrasts.
             Corrected bugs in the call and with the boundary box in cat_main.
             Added simple skull-stripping for non-T1 data in cat_main_updateSPM.
             Corrected small problems PD/T2 processing in cat_vol_partvol.
             Updated cat_main_gintnorm with k-means peaks rather than SPM peaks
             in the backup/T2/PD stream - it is ok but could be better.
             Added high accuracy (smaller spm.tol values) in cases of failed
             SPM preprocessing 1 in cat_run_job.
             Updated simple LAS function but it is still unstable and turned off.
(2) Fixed:   Corrected bug in cat_vol_sanlm for images with negative values.
(3) Fixed:   Corrected bug of matrix size for different template size in
             cat_main_registration.
(4) Fixed:   Corrected resolution rounding issue in cat_run[1639].
(5) New:     Added output of unprocessed files.
(6) Fixed:   Tiny corrections in cat_vol_qa,
(7) Fixed:   Corrected typo in cat_surf_render2.


------------------------------------------------------------------------
r1833 | gaser | 2021-05-28 13:03:26 +0200 (Fri, 28 May 2021) | 16 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_vol_display_label.m
M       html/cat.html
M       html/cat_methods_RBM.html
M       html/cat_versions.html
MM      standalone/cat_standalone_deface.txt
MM      standalone/cat_standalone_dicom2nii.txt

(1) Changed: Updated CAT12 manual and version information.
(2) Fixed:   Corrected references in cat_methods_RBM.html.
(3) Fixed:   Corrected prepended name of atlases in cat_vol_display_label.m.


------------------------------------------------------------------------
r1832 | gaser | 2021-05-28 12:37:07 +0200 (Fri, 28 May 2021) | 26 lines

Changed paths:
M       CHANGES.txt
M       Contents_info.txt
M       cat_conf_ROI.m
M       cat_defaults.m
M       cat_run.m
MM      development/Atlas_correct_scaling.m
M       html/cat_licences.html
M       html/cat_methods_RBM.html
M       standalone/cat_standalone.sh
M       standalone/cat_standalone_segment.txt
M       standalone/cat_standalone_segment_long.txt
M       standalone/cat_standalone_simple.txt
A       templates_MNI152NLin2009cAsym/thalamus.csv
A       templates_MNI152NLin2009cAsym/thalamus.nii
A       templates_MNI152NLin2009cAsym/thalamus.txt
A       templates_external/MNI152NLin2009cSym.nii
A       templates_external/y_MNI152NLin2009cSym_to_MNI152NLin2009cAsym.nii

(1) Changed: Changed default atlases in cat_defaults.m.
(2) Fixed:   Added missing check for shooting template to cat_run.m.
(3) Added:   Added new atlas of thalamic nuclei.
(4) Added:   Added MNI152NLin2009cSym.nii and its deformation field to
             templates_external.


------------------------------------------------------------------------
r1831 | gaser | 2021-05-28 00:50:12 +0200 (Fri, 28 May 2021) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_cat.sh
M       standalone/cat_parallelize.sh
M       standalone/cat_standalone.sh
A       standalone/cat_standalone_deface.txt
A       standalone/cat_standalone_dicom2nii.txt
M       standalone/cat_standalone_resample.txt
M       standalone/cat_standalone_segment.txt
M       standalone/cat_standalone_segment_long.txt
M       standalone/cat_standalone_smooth.txt
M       standalone/cat_standalone_tfce.txt

(1) Changed: Updated standalone tools to easier use additional arguments.
(2) Changed: Updated help text and examples for standalone tools.
(3) Added:   Added standalone tools for dicom import and de-facing.


------------------------------------------------------------------------
r1830 | gaser | 2021-05-27 18:15:21 +0200 (Thu, 27 May 2021) | 18 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cat_simple.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_results.m
M       cat_vol_headtrimming.m
M       standalone/cat_standalone_segment.txt
M       standalone/cat_standalone_segment_long.txt
M       standalone/cat_standalone_simple.txt

(1) Changed: Updated standalone tools to new release.
(2) Changed: Prepared head trimming tool for categorical data (e.g. atlases).
(3) Changed: Updated cat_simple to new release.
(4) Changed: Updated checklist in Makefile.
(5) Fixed:   Added check for number of structures in csv atlas file and xml data
             file.

------------------------------------------------------------------------
r1829 | gaser | 2021-05-27 11:40:22 +0200 (Thu, 27 May 2021) | 46 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_batch_cat.sh
M       cat_conf_factorial.m
M       cat_run.m
M       cat_surf_createCS2.m
M       cat_surf_info.m
M       cat_update.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_ui.m
D       development/Anatomy2CAT12.m
        > moved to development/Atlas_Anatomy2CAT12.m
A  +    development/Atlas_Anatomy2CAT12.m
        > moved from development/Anatomy2CAT12.m
A  +    development/Atlas_JulichBrain2CAT12.m
        > moved from development/JulichBrain2CAT12.m
A       development/Atlas_correct_scaling.m
A  +    development/Atlas_summarize_MPM.m
        > moved from development/ROI_summarize_MPM.m
D       development/JulichBrain2CAT12.m
        > moved to development/Atlas_JulichBrain2CAT12.m
D       development/ROI_summarize_MPM.m
        > moved to development/Atlas_summarize_MPM.m
M       html/cat_starting.html
M       slice_overlay.m
M       templates_MNI152NLin2009cAsym/cobra.nii
M       templates_MNI152NLin2009cAsym/hammers.nii
M       templates_MNI152NLin2009cAsym/ibsr.nii
M       templates_MNI152NLin2009cAsym/lpba40.nii
M       templates_MNI152NLin2009cAsym/neuromorphometrics.nii

(1) Changed: Updated scaling factors for atlases.
(2) Changed: Some minor formatting to slice_overlay.m.
(3) Changed: Updated quick start guide.
(4) Changed: Renamed all atlas-related functions in development.
(5) Changed: Added option for voxel-wise covariate to flexible factorial design.
(6) Changed: Updated examples in cat_vol_slice_overlay_ui.m
(7) Changed: Changed order of commands in example in cat_batch_cat.sh.
(8) Changed: Updated handling of log-scaled maps in cat_vol_slice_overlay.m and
             added dialog with predefiend thresholds.

(9) Added:   Atlas_correct_scaling.m to correct scaling factor of atlases.
(10) Fixed:  Corrected default template folder in cat_update.m.
(11) Fixed:  Corrected template folder for 32k meshes in cat_surf_info.m

------------------------------------------------------------------------
r1828 | gaser | 2021-05-20 22:53:18 +0200 (Thu, 20 May 2021) | 20 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_cat.sh
M       cat_conf_extopts.m
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_long_main.m
M       cat_surf_map_atlas.m
MM      development/Atlas_ROI_tissue.m
M       html/cat.html
M       tbx_cfg_cat.m
M       templates_MNI152NLin2009cAsym/neuromorphometrics.nii

(1) Changed: Added parameter bb to cat_defaults for easier use.
(2) Changed: Updated help text.
(3) Changed: Updated printout for log-file in cat_batch_cat.sh.
(4) Fixed:   Corrected default setttings in cat_conf_long.m if job is not
             available.

------------------------------------------------------------------------
r1827 | gaser | 2021-05-19 15:56:05 +0200 (Wed, 19 May 2021) | 17 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_batch_cat.sh
M       cat_surf_results.m
M       cat_vol_createMPM.m
M       cat_vol_slice_overlay.m
M       html/cat.html

(1) Changed: Added field to define labels that should be excluded from atlas
             in cat_vol_createMPM.m
(2) Changed: Changed tick-labels for log-scaled colorbars and removed white
             borders in cat_vol_slice_overlay.m
(3) Changed: Changed tick-labels for log-scaled colorbars in cat_surf_results.m.
(4) Changed: Some small modifications in cat_batch_cat.sh and Makefile.

------------------------------------------------------------------------
r1826 | gaser | 2021-05-17 17:38:07 +0200 (Mon, 17 May 2021) | 22 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_defaults.m
M       cat_stat_analyze_ROIs.m
M       cat_vol_imcalc.m
A       development/Atlas_ROI_tissue.m
M       html/cat.html
M       templates_MNI152NLin2009cAsym/cobra.csv
M       templates_MNI152NLin2009cAsym/hammers.csv
M       templates_MNI152NLin2009cAsym/ibsr.csv
M       templates_MNI152NLin2009cAsym/lpba40.csv
M       templates_MNI152NLin2009cAsym/mori.csv
M       templates_MNI152NLin2009cAsym/neuromorphometrics.csv

(1) Changed: Updated volume atlas information about availability of local
             volumes for GM, WM, and CSF and added field to csv-files and
             updated cat_defaults.
(2) Changed: cat_stat_analyze_ROIs now only analyses ROIs for specific tissue
             types if defined.


------------------------------------------------------------------------
r1825 | gaser | 2021-05-16 23:48:54 +0200 (Sun, 16 May 2021) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_createCS2.m
M       cat_surf_parameters.m
M       cat_surf_results.m
 M      development/ROI_summarize_MPM.m
M       html/cat.html
 M      templates_MNI152NLin2009cAsym/brainmask_T1.nii

(1) Changed: Surface without overlay are now also displayed with
             cat_surf_results.m
(2) Changed: Sulcual depth can now also be estimated for pial surfaces.
(3) Fixed:   Subfunction cat_surf_createCS2wdcd in cat_surf_createCS2.m did not
             work.

------------------------------------------------------------------------
r1824 | gaser | 2021-05-12 17:47:31 +0200 (Wed, 12 May 2021) | 33 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_factorial.m
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_long_multi_run.m
M       cat_plot_boxplot.m
M       cat_stat_check_cov.m
M       cat_stat_spm.m
M       cat_surf_createCS2.m
M       cat_surf_resamp_freesurfer.m
M       cat_surf_results.m
M       cat_vol_ROI_summarize.m
M       cat_vol_createMPM.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_ui.m

(1) Changed: Updated cat_vol_slice_overlay to support deviating thresholds of
             log-scaled p-values.
(2) Changed: Added optional masking to cat_vol_create_MPM.m and changed
             thresholds and median apporach and added support for writing 4D
             probability maps.
(3) Changed: Some small modifications to cat_surf_results.m
(4) Changed: Changed underling surface type in cat_stat_spm.m
(5) Fixed:   Added missing bracket to cat_long_multi_run.m
(6) Fixed:   Corrected wrong call for fontsize in cat_plot_boxplot.m
(7) Fixed:   Estimation of data range for meshes in cat_stat_check_cov.m was
             not working.
(8) Fixed:   Create folder if necessary for cat_surf_resamp_freesurfer.m
(9) Changed: Renamed mTemplate_T1.nii to Template_T1_masked.nii and changed
             links in scripts to that file.


------------------------------------------------------------------------
r1823 | gaser | 2021-05-12 17:32:40 +0200 (Wed, 12 May 2021) | 60 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_batch_cat.sh
M       cat_batch_long.sh
M       cat_batch_spm.sh
M       development/Anatomy2CAT12.m
M       development/JulichBrain2CAT12.m
A       development/ROI_summarize_MPM.m
M       html/cat.html
M       html/cat_licences.html
M       html/cat_methods_RBM.html
M       html/cat_versions.html
M       templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.csv
M       templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.csv
M       templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.csv
A  +    templates_MNI152NLin2009cAsym/Template_T1_masked.nii
        > moved from templates_MNI152NLin2009cAsym/mTemplate_T1.nii
M       templates_MNI152NLin2009cAsym/aal3.csv
M       templates_MNI152NLin2009cAsym/aal3.txt
M       templates_MNI152NLin2009cAsym/anatomy3.nii
A       templates_MNI152NLin2009cAsym/brainmask_T1.nii
M       templates_MNI152NLin2009cAsym/cobra.csv
M       templates_MNI152NLin2009cAsym/cobra.nii
M       templates_MNI152NLin2009cAsym/cobra.txt
M       templates_MNI152NLin2009cAsym/hammers.csv
M       templates_MNI152NLin2009cAsym/hammers.nii
M       templates_MNI152NLin2009cAsym/hammers.txt
M       templates_MNI152NLin2009cAsym/ibsr.csv
M       templates_MNI152NLin2009cAsym/ibsr.nii
M       templates_MNI152NLin2009cAsym/ibsr.txt
M       templates_MNI152NLin2009cAsym/julichbrain.csv
M       templates_MNI152NLin2009cAsym/julichbrain.nii
M       templates_MNI152NLin2009cAsym/julichbrain.txt
M       templates_MNI152NLin2009cAsym/lpba40.csv
M       templates_MNI152NLin2009cAsym/lpba40.nii
M       templates_MNI152NLin2009cAsym/lpba40.txt
D       templates_MNI152NLin2009cAsym/mTemplate_T1.nii
        > moved to templates_MNI152NLin2009cAsym/Template_T1_masked.nii
M       templates_MNI152NLin2009cAsym/mori.csv
M       templates_MNI152NLin2009cAsym/mori.txt
M       templates_MNI152NLin2009cAsym/neuromorphometrics.csv
M       templates_MNI152NLin2009cAsym/neuromorphometrics.nii
M       templates_MNI152NLin2009cAsym/neuromorphometrics.txt
M       templates_MNI152NLin2009cAsym/schaefer.txt
M       templates_MNI152NLin2009cAsym/templates.man

(1) Changed: Updated atlas text in version information and description.
(2) Changed: Added brainmask_T1.nii to templateb folder.
(3) Changed: Updated information about templates.
(4) Changed: Updated hammers atlas to new version with 95 regions.
(5) Changed: Updated neuromorphometrics atlas by estimating maximum probability
             maps.
(6) Changed: Updated julicbrain atlas to version v2.6.
(7) Changed: Some small modifications to scripts for creating anatomy and
             julichbrain atlas.
(8) Fixed:   Call of shell scripts from relative path is now working.


------------------------------------------------------------------------
r1822 | dahnke | 2021-05-12 16:58:19 +0200 (Wed, 12 May 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_run_job1639.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_vol_qa.m
M       templates_animals/ape_greater_cat.nii

(1) Fixed:   Corrected affine registration bug in primates.
(2) Fixed:   Setup using the new cat_main pipeline in case of non-T1 contrast.

------------------------------------------------------------------------
r1821 | gaser | 2021-05-05 11:27:01 +0200 (Wed, 05 May 2021) | 23 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_conf_output.m
M       cat_main_write.m
M       cat_surf_parameters.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_ui.m
M       html/cat.html
M       html/cat_versions.html

(1) Changed: Updated atlas text in version information.
(2) Changed: Added masked template as example to cat_vol_slice_overlay_ui.m and
             added examples for font size and use of subfolders for naming
             saved image files.
(3) Changed: If an atlas map is saved in native space the corresponding csv-file
             is now also saved.
(4) Changed: Added options to save atlas maps in developer mode.
(5) Changed: Corrected use of thresholds (gt vs ge) for log-scaled p-values in
             cat_vol_slice_overlay.m and added options for font size and use of
             subfolders for getting filename to save images.

------------------------------------------------------------------------
r1820 | gaser | 2021-05-03 00:27:25 +0200 (Mon, 03 May 2021) | 26 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_conf_output.m
M       cat_io_writenii.m
M       cat_long_multi_run.m
M       cat_main_write.m
M       cat_stat_check_cov.m
M       cat_vol_slice_overlay.m
M       html/cat.html
M       templates_MNI152NLin2009cAsym/templates.man

(1) Changed: Updated options and help text for atlas maps.
(2) Changed: Renamed saved cat atlas to cat_* to have consistent atlas names
             if saved in native space.
(3) Changed: Hide SRP GUI for default users.
(4) Fixed:   For deplyed version the file cat_long_main.m might be read-only.
             Therefore, this file should be replaced after installation (thanks
             to Dimitri Papadopoulos for pointing to that issue).
(5) Fixed:   Comparisons for threshold in cat_vol_slice_overlay were corrected
             to ">" instead of ">=" (thanks to Pravesh Parekh for pointing to
             that issue).
(6) Fixed:   Corrected list of filenames in cat_stat_check_cov.m


------------------------------------------------------------------------
r1819 | gaser | 2021-04-30 22:01:02 +0200 (Fri, 30 Apr 2021) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_main1639.m
M       cat_main_write.m
M       cat_stat_check_cov.m
MM      cat_stat_getCSVXMLfield.m

(1) Fixed:   Corrected index error in cat_stat_check_cov.m.
(2) Changed: Use job.extopts.AMAPframing by default.
(3) Changed: Save individual atlas maps now always in mri and not mri_atlas.


------------------------------------------------------------------------
r1818 | gaser | 2021-04-30 18:36:42 +0200 (Fri, 30 Apr 2021) | 22 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_factorial.m
M       cat_main_amap.m
M       cat_main_amap1639.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       html/cat.html
M       html/cat_starting.html
M       html/cat_versions.html

(1) Changed: Changed default parameters for Amap to 10 iterations and block
             size of 64/mean(voxelsize).
(2) Changed: Updated version information and CAT12 manual.
(3) Changed: Updated block size and iterations for AMAP in cat_main_amap*m.
(4) Changed: Updated help text for new basic models function.
(4) Fixed:   Corrected path for xml-file for longitudinal batch in
             cat_surf_createCS*m.

------------------------------------------------------------------------
r1817 | dahnke | 2021-04-29 17:11:43 +0200 (Thu, 29 Apr 2021) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_main1639.m
M       cat_main_amap.m
M       cat_main_amap1639.m
M       cat_main_write.m
M       cat_plot_boxplot.m
A       cat_stat_getCSVXMLfield.m
M       cat_vol_reduceRes.m
M       html/cat_methods_templates.html

(1) Changed:    Updated AMAP functionality to stabilize the segmentation
                (use experimental option).
(2) New:        Added boxplot batch for XML data.
(3) New:        Added CSV/XML input batch.
(4) Fixed:      Corrected bug in expert atlas export mapping in cat_main_write.

------------------------------------------------------------------------
r1816 | gaser | 2021-04-29 17:03:37 +0200 (Thu, 29 Apr 2021) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_main_amap.m
M       cat_main_amap1639.m
M       cat_surf_createCS2.m

(1) Changed: Changed default parameters for Amap to 10 iterations and block
             size of 64/mean(voxelsize).
(2) Fixed:   Euler characteristic and defect size were not correct for
             longitudinal batch.


------------------------------------------------------------------------
r1815 | gaser | 2021-04-28 15:49:25 +0200 (Wed, 28 Apr 2021) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_cat.sh
M       cat_io_writenii.m
M       tbx_cfg_cat.m

(1) Changed: Deselected warps-field in cat_batch_cat.sh to prevent that
             nonlinear registration is called if no normalized data are saved.
(2) Fixed:   Corrected image filter in tbx_cfg_cat.m that caused issues with old
             batches.


------------------------------------------------------------------------
r1814 | gaser | 2021-04-27 12:50:38 +0200 (Tue, 27 Apr 2021) | 21 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cat_conf_long.m
M       cat_conf_output.m
M       cat_defaults.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_vol_partvol.m
M       cat_vol_partvol1639.m
M       html/cat.html

(1) Changed: Disabled use of BIDS folder for longitudinal batch.
(2) Changed: Removed BIDS option from defaults.
(3) Fixed:   Also recognize lesion mask with Inf and NaN fpr SLC option.
(4) Fixed:   YslA had wrong data format in cat_vol_partvol*m.
(5) Fixed:   Path for useprior option was wrong in cat_surf_createCS*m.


------------------------------------------------------------------------
r1813 | gaser | 2021-04-23 01:03:43 +0200 (Fri, 23 Apr 2021) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_check_cov.m

Fixed:  Corrected some minor bugs in cat_stat_check_cov.m.

------------------------------------------------------------------------
r1812 | gaser | 2021-04-23 00:13:50 +0200 (Fri, 23 Apr 2021) | 26 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_defaults.m
M       cat_parallelize.m
M       cat_plot_cov.m
M       cat_stat_check_cov.m
M       cat_stat_spm2x.m
M       cat_surf_render.m
M       cat_surf_render2.m
M       cat_surf_results.m
M       html/cat.html

(1) Changed: Added surface renderings to cat_stat_check_cov.m and cleaned
             global parameters
(2) Changed: Some slight changes to cat_surf_results for better data checking.
(3) Changed: Exclude NaNs if surface information is estimated in
             cat_surf_render2.m.
(4) Changed: Added flag for group to code samples in cat_plot_cov.m and
             optimized output of filenames in plot.
(5) Changed: Changed defaults for SRP and writing deformations.
(6) Fixed:   Use stamdard Pmesh from cat_surf_info in cat_stat_spm2x.m for
             getting mesh structure.


------------------------------------------------------------------------
r1811 | gaser | 2021-04-21 17:14:12 +0200 (Wed, 21 Apr 2021) | 23 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cat_batch_long.sh
M       cat_conf_extopts.m
M       cat_conf_long.m
M       cat_long_main.m
M       cat_long_multi_run.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_update.m
M       templates_MNI152NLin2009cAsym/anatomy3.csv

(1) Changed: Updated targets in Makefile.
(2) Changed: Added "enablepriors" flag to longitudinal pipeline in expert mode
             to optionally disable use of priors.
(3) Changed: Updated help text.
(4) Changed: Updated flags in cat_batch_long.sh.
(5) Fixed:   Corrected BIDS paths in cat_surf_createCS*.m.
(6) Fixed:   Corrected anatomy3.csv because left and right hemisphere had the
             same IDs (thanks to Michael Firbank for pointing to that issue).


------------------------------------------------------------------------
r1810 | gaser | 2021-04-19 18:49:20 +0200 (Mon, 19 Apr 2021) | 15 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_conf_output.m
M       cat_io_data2mat.m
M       cat_run.m
M       html/cat_versions.html
M       tbx_cfg_cat.m

(1) Changed: Added "img" to data filter for segmentation.
(2) Changed: Updated version information in html and CAT12 manual.
(3) Changed: Added check that log-files were not deleted in cat_run.m.
(4) Changed: Added structure array to cat_io_data2mat.m to save surface
             or resampled volume structure.

------------------------------------------------------------------------
r1809 | gaser | 2021-04-18 11:25:21 +0200 (Sun, 18 Apr 2021) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main1639.m
M       cat_main_correctmyelination.m
M       cat_run.m

Fixed:  Corrected typos.

------------------------------------------------------------------------
r1808 | dahnke | 2021-04-17 23:03:00 +0200 (Sat, 17 Apr 2021) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main1639.m
M       cat_main_correctmyelination.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_run.m
M       cat_surf_resamp.m

(1) New:     Added lazy option to avoid checking of parameters.
(2) Fixed:   Corrected myelination settings and updates of the correction.
(3) Fixed:   Corrected error in report figure in case of position updates.
             However, it was not possible to avoid the SPM overlay box.



------------------------------------------------------------------------
r1807 | gaser | 2021-04-17 13:50:59 +0200 (Sat, 17 Apr 2021) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       cat_main1639.m
M       html/cat.html

Fixed:  Fixed use of LASmyostr parameter in cat_main.m and cat_main1639.m

------------------------------------------------------------------------
r1806 | gaser | 2021-04-16 21:01:26 +0200 (Fri, 16 Apr 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_conf_tools.m
M       cat_io_data2mat.m
M       html/cat.html

(1) Fixed:   Corrected handling of LASmyostr parameter.
(2) Changed: Updated help text.

------------------------------------------------------------------------
r1805 | gaser | 2021-04-16 16:27:00 +0200 (Fri, 16 Apr 2021) | 12 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_surf_info.m
M       cat_surf_parameters.m

(1) Changed: Added option to additionally transform sulcal depth with
             sqrt-function (which was available as default in older
             versions).
(2) Changed: Update CAT12 manual.

------------------------------------------------------------------------
r1804 | gaser | 2021-04-15 22:40:54 +0200 (Thu, 15 Apr 2021) | 7 lines

Changed paths:
M       CHANGES.txt
MM      cat_conf_factorial.m

Fixed:  Fixed output field in cat_conf_factorial.m to not break subsequent batch
        with orthogonlity check.

------------------------------------------------------------------------
r1803 | gaser | 2021-04-15 22:24:33 +0200 (Thu, 15 Apr 2021) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_factorial.m
M       cat_surf_results.m
M       html/cat.html

Changed: Some minor changes to cat_surf_results.m and cat_conf_factorial.m

------------------------------------------------------------------------
r1802 | gaser | 2021-04-15 21:03:25 +0200 (Thu, 15 Apr 2021) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
A       cat_conf_factorial.m
M       cat_io_data2mat.m
M       cat_stat_factorial_design.m
M       cat_stat_spm.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Added:   Added new batch for factorial designs for VBM that skips many
             options that are not needed for VBM. There are two models
             available for cross-sectional and longitudinal data.
(2) Changed: Some smaller changes to cat_stat_spm.m and cat_io_data2mat.m.
(3) Changed: Updated basic design that is called from CAT12 GUI.

------------------------------------------------------------------------
r1801 | gaser | 2021-04-14 16:47:05 +0200 (Wed, 14 Apr 2021) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_run_newcatch.m
M       html/cat.html

Fixed: Corrected error messages for Piwik.


------------------------------------------------------------------------
r1800 | gaser | 2021-04-14 16:13:23 +0200 (Wed, 14 Apr 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_run_newcatch.m
M       html/cat.html

(1) Changed: Added field "TotalUsers" to Piwik information to obtain a relaible
             count of overall users.
(2) Changed: Added release number to error messages for Piwik.

------------------------------------------------------------------------
r1799 | gaser | 2021-04-09 13:01:51 +0200 (Fri, 09 Apr 2021) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat12.m

Fixed: Typo in cat12.m caused crash.

------------------------------------------------------------------------
r1798 | gaser | 2021-04-09 12:46:29 +0200 (Fri, 09 Apr 2021) | 18 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_conf_tools.m
M       cat_stat_check_cov.m
M       cat_stat_check_cov2.m
M       html/cat.html
M       html/cat_versions.html
M       spm_cat12.m

(1) Changed: Updated CAT12 manual.
(2) Changed: Replaced Mahalanobis distance for quqlity check by ratio bezween
             IQR and mean correlation.
(3) Changed: Changed version to CAT12.8-Beta and updated version information.


------------------------------------------------------------------------
r1797 | gaser | 2021-04-09 11:33:35 +0200 (Fri, 09 Apr 2021) | 17 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_ROI.m
M       cat_conf_extopts.m
M       cat_conf_opts.m
M       cat_conf_tools.m
RM +    cat_io_subfolders.m
M       cat_roi_fun.m
M       cat_stat_cva_ui.m
M       html/cat.html

(1) Changed: Updated help text.
(2) Changed: Added/removed some functions to CAT12 GUI.
(3) Changed: Set default value for myelin correction to 0.

------------------------------------------------------------------------
r1796 | gaser | 2021-04-08 11:14:18 +0200 (Thu, 08 Apr 2021) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
RM +    cat_io_subfolders.m
M       cat_stat_nanmean.m
M       cat_stat_nanmedian.m
M       cat_stat_nanstd.m
M       cat_stat_nansum.m
M       html/cat.html

(1) Fixed:   Corrected typos.
(2) Changed: Added tool for saving volume or surface data as mat-file to GUI.


------------------------------------------------------------------------
r1795 | dahnke | 2021-04-07 20:59:26 +0200 (Wed, 07 Apr 2021) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_updateSPM.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_stat_nanmean.m
M       cat_stat_nanmedian.m
M       cat_stat_nanstd.m
M       cat_stat_nansum.m

(1) Fixed:   Corrected affeg problem in case of MT data.
(2) Fixed:   Corrected smaller bugs in cat_run, cat_main, cat_main_updateSPM.
(3) Changed: Small update of cat_stat_nan[mean|std|median|sum].


------------------------------------------------------------------------
r1794 | gaser | 2021-04-07 17:11:36 +0200 (Wed, 07 Apr 2021) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
R       cat_io_subfolders.m
M       html/cat.html

Fixed: Resolved issue svn with cat_io_subfolders.m

------------------------------------------------------------------------
r1793 | gaser | 2021-04-07 01:30:18 +0200 (Wed, 07 Apr 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_long_biascorr.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m

(1) Fixed:   Corrected wrong path for useprior in cat_surf_createCS.m and
             cat_surf_createCS2.m.
(2) Changed: Updated help text.


------------------------------------------------------------------------
r1792 | gaser | 2021-04-06 15:08:16 +0200 (Tue, 06 Apr 2021) | 10 lines

Changed paths:
M       CHANGES.txt
A       cat_io_subfolders.m
M       cat_surf_createCS2.m

(1) Fixed:   Added missing cat_io_subfolder.m.
(2) Fixed:   Variable etime was not defined for usepior flag in
             cat_surf_createCS2.m


------------------------------------------------------------------------
r1791 | gaser | 2021-04-06 11:15:54 +0200 (Tue, 06 Apr 2021) | 280 lines

Changed paths:
M       Amap.c
M       Bayes.c
M       BayesMex.c
M       CHANGES.txt
M       Contents.m
M       Contents_info.txt
M       Kmeans.c
M       KmeansMex.c
M       MrfPrior.c
M       Pve.c
M       WarpPriors.c
M       cat12.m
M       cat12.sh
M       cat_amap.c
M       cat_amap.m
M       cat_batch_cat.m
M       cat_batch_cat.sh
M       cat_batch_long.m
M       cat_batch_long.sh
M       cat_batch_spm.m
M       cat_batch_spm.sh
M       cat_check.m
M       cat_check_system_output.m
M       cat_conf_ROI.m
M       cat_conf_catsimple.m
M       cat_conf_extopts.m
M       cat_conf_long.m
M       cat_conf_nonlin_coreg.m
M       cat_conf_opts.m
M       cat_conf_output.m
M       cat_conf_stools.m
M       cat_conf_stoolsexp.m
M       cat_conf_tools.m
M       cat_debug.m
M       cat_defaults.m
M       cat_display_matlab_PID.m
M       cat_get_defaults.m
M       cat_install_atlases.m
M       cat_install_tfce.m
M       cat_io_FreeSurfer.m
M       cat_io_addwarning.m
M       cat_io_cgw2seg.m
M       cat_io_checkdepfiles.m
M       cat_io_checkinopt.m
M       cat_io_cmd.m
M       cat_io_colormaps.m
M       cat_io_cprintf.m
M       cat_io_csv.m
M       cat_io_data2mat.m
M       cat_io_findjobj.m
M       cat_io_handle_pre.m
M       cat_io_img2nii.m
M       cat_io_lazy.m
M       cat_io_matlabversion.m
M       cat_io_mergeStruct.m
M       cat_io_remat.m
M       cat_io_report.m
M       cat_io_rerun.m
M       cat_io_rmdir.m
M       cat_io_seg2cgw.m
M       cat_io_send_to_server.m
M       cat_io_senderrormail.m
M       cat_io_strrep.m
M       cat_io_struct2table.m
M       cat_io_updateStruct.m
M       cat_io_volctype.m
M       cat_io_writenii.m
M       cat_io_xml.m
M       cat_io_xml2csv.m
M       cat_long_APP.m
M       cat_long_biascorr.m
M       cat_long_createTPM.m
M       cat_long_main.m
M       cat_long_multi_run.m
M       cat_long_shoot_defaults.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_APRG.m
M       cat_main_LAS.m
M       cat_main_LAS2.m
M       cat_main_LAS21639.m
M       cat_main_LASs.m
M       cat_main_amap.m
M       cat_main_amap1639.m
M       cat_main_clean_gwc.m
M       cat_main_clean_gwc1639.m
M       cat_main_cleanup.m
M       cat_main_correctmyelination.m
M       cat_main_gcut.m
M       cat_main_gcut_DEV.m
M       cat_main_gintnorm.m
M       cat_main_gintnorm1639.m
M       cat_main_gintnormi.m
M       cat_main_kamap.m
M       cat_main_registration.m
M       cat_main_registration2.m
M       cat_main_reportcmd.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_main_roi.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_main_updateWMHs.m
M       cat_main_update_intnorm.m
M       cat_main_write.m
M       cat_ornlm.c
M       cat_ornlm.m
M       cat_parallelize.m
M       cat_plot_boxplot.m
M       cat_plot_circular.m
M       cat_plot_cov.m
M       cat_roi_fun.m
M       cat_roi_roi2surf.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_run_job_APP_SPMfinal.m
M       cat_run_job_APP_SPMinit.m
M       cat_run_job_APP_init.m
M       cat_run_job_APP_init1070.m
M       cat_run_job_APRGs.m
M       cat_run_job_multiTPM.m
M       cat_run_newcatch.m
M       cat_sanlm.c
M       cat_sanlm.m
M       cat_simple.m
M       cat_spm_affreg.m
M       cat_spm_preproc8.m
M       cat_spm_preproc_run.m
M       cat_spm_preproc_write8.m
M       cat_spm_results_ui.m
M       cat_spm_shoot_template.m
M       cat_spm_smoothto8bit.m
M       cat_stat_IQR.m
M       cat_stat_TIV.m
M       cat_stat_analyze_ROIs.m
M       cat_stat_calc_stc.m
M       cat_stat_check_SPM.m
M       cat_stat_check_cov.m
M       cat_stat_check_cov2.m
M       cat_stat_confplot_spm.m
M       cat_stat_cva_ui.m
M       cat_stat_diff.m
M       cat_stat_factorial_design.m
M       cat_stat_histth.m
M       cat_stat_kmeans.m
M       cat_stat_marks.m
M       cat_stat_nanmean.m
M       cat_stat_nanmedian.m
M       cat_stat_nanstat1d.m
M       cat_stat_nanstd.m
M       cat_stat_nansum.m
M       cat_stat_polynomial.m
M       cat_stat_showslice_all.m
M       cat_stat_spm.m
M       cat_stat_spm2x.m
M       cat_surf_GI3D.m
M       cat_surf_avg.m
M       cat_surf_calc.m
M       cat_surf_coregvol2surf.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_create_TPM_hull_surface.m
M       cat_surf_display.m
M       cat_surf_epivolsurf.m
M       cat_surf_flipsides.m
M       cat_surf_fun.m
M       cat_surf_gyrification.m
M       cat_surf_info.m
M       cat_surf_load.m
M       cat_surf_map_atlas.m
M       cat_surf_max.m
M       cat_surf_parameters.m
M       cat_surf_rename.m
M       cat_surf_render.m
M       cat_surf_render2.m
MM      cat_surf_renderv.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
M       cat_surf_results.m
M       cat_surf_scaling.m
M       cat_surf_smooth.m
M       cat_surf_surf2roi.m
M       cat_surf_vol2surf.m
M       cat_surf_vx2surf.m
M       cat_system.m
M       cat_tst_BWPsliceartifact.m
M       cat_tst_CJV.m
M       cat_tst_calc_kappa.m
M       cat_tst_cattest.m
M       cat_tst_qa_cleaner.m
M       cat_tst_staple_multilabels.m
M       cat_update.m
M       cat_vbdist.c
M       cat_vbdist.m
M       cat_version.m
M       cat_vol_ROI_summarize.m
M       cat_vol_ROIval.c
M       cat_vol_ROIval.m
M       cat_vol_approx.m
M       cat_vol_avg.m
M       cat_vol_correct_slice_scaling.m
M       cat_vol_createMPM.m
M       cat_vol_createTPM.m
M       cat_vol_ctype.m
M       cat_vol_defs.m
M       cat_vol_display_label.m
M       cat_vol_div.m
M       cat_vol_downcut.c
M       cat_vol_downcut.m
M       cat_vol_eidist.c
M       cat_vol_eidist.m
M       cat_vol_eikonal3.c
M       cat_vol_eikonal3.m
M       cat_vol_findfiles.m
M       cat_vol_genus0.c
M       cat_vol_genus0.m
M       cat_vol_grad.m
M       cat_vol_gradient3.c
M       cat_vol_groupwise_ls.m
M       cat_vol_headtrimming.m
M       cat_vol_imcalc.m
M       cat_vol_interp3f.m
M       cat_vol_iscale.m
M       cat_vol_iscaling.m
M       cat_vol_laplace3.c
M       cat_vol_laplace3.m
M       cat_vol_laplace3R.c
M       cat_vol_laplace3R.m
M       cat_vol_localstat.c
M       cat_vol_localstat.m
M       cat_vol_maskimage.m
M       cat_vol_median3.c
M       cat_vol_median3.m
M       cat_vol_median3c.c
M       cat_vol_median3c.m
M       cat_vol_morph.m
M       cat_vol_nanmean3.m
M       cat_vol_nonlin_coreg.m
M       cat_vol_nonlin_coreg_multi_run.m
M       cat_vol_partvol.m
M       cat_vol_partvol1639.m
M       cat_vol_pbt.m
M       cat_vol_pbt2.m
M       cat_vol_pbt3.m
M       cat_vol_pbtp.c
M       cat_vol_pbtp.cpp
M       cat_vol_pbtp.m
M       cat_vol_pbtp2.c
M       cat_vol_pbtv.cpp
M       cat_vol_qa.m
M       cat_vol_reduceRes.m
M       cat_vol_resize.m
M       cat_vol_sanlm.m
M       cat_vol_series_align.m
M       cat_vol_set_com.m
M       cat_vol_simgrow.c
M       cat_vol_simgrow.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_rgb_ui.m
M       cat_vol_slice_overlay_ui.m
M       cat_vol_smooth3X.m
M       cat_vol_testflipping.m
M       cat_vol_urqio.m
M       check_pipeline.sh
M       distribute_to_server.sh
M       genus0.c
M       html/cat.html
M       optimizer3d.c
M       ornlm_float.c
M       sanlm_float.c
M       tbx_cfg_cat.m
M       vollib.c

(1) Changed: Added BIDS support to save subfolders in BIDS structure.
(2) Changed: Updated and cleaned cat_batch_cat.m.
(3) Changed: Added/edited header in all files to provide copyright information.
(4) Changed: Added support for nii.gz files for core segmentation.

------------------------------------------------------------------------
r1790 | dahnke | 2021-04-05 20:40:34 +0200 (Mon, 05 Apr 2021) | 28 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_correctmyelination.m
M       cat_main_reportfig.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m
M       cat_vol_groupwise_ls.m
M       cat_vol_pbt.m

(1) Fixed:    Corrected bug in long pipeline in cat_vol_groupwise_ls.
(2) Fixed.    Corrected opengl setting in cat_main_reportfig.
(3) Fixed:    Corrected setting of extended Ypp map in cat_vol_pbt and
              cat_surf_createS2.
(4) Changed:  Splitt of LASmyostr from LASstr parameter for further
              test in the developer mode in cat_conf_extopts, cat_main,
              and cat_main1639.
(5) Changed:  Further regional limitation of the LAS myelination correction
              in the amygdala and hippocampus. Larger dilatation of the sub-
              cortical regions to limit corrections in the insula.
(6) Changed:  Added temporar test block to optimize the white/pial surfaces
              via surface deformation that is not working yet.
(7) Changed:  Further corrections to improve surface optimization (SRP21+)
              in cat_surf_createCS2 and cat_surf_fun.


------------------------------------------------------------------------
r1789 | gaser | 2021-03-29 11:32:27 +0200 (Mon, 29 Mar 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_long.m
M       cat_batch_long.sh
M       cat_conf_extopts.m

(1) Changed: Updated help text.
(2) Fixed:   Corrected typo in cat_batch_long.m that pevented to show error
             messages.


------------------------------------------------------------------------
r1788 | gaser | 2021-03-28 16:42:17 +0200 (Sun, 28 Mar 2021) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
MM      cat_io_data2mat.m
MM      cat_plot_cov.m
M       cat_surf_createCS.m
M       cat_surf_info.m
M       html/cat.html
 M      templates_MNI152NLin2009cAsym/mTemplate_T1.nii

(1) Fixed:   Added check for useprior to etime command in cat_surf_createCS.m.
(2) Fixed:   Replace old Template surface name in cat_surf_info.m.


------------------------------------------------------------------------
r1787 | dahnke | 2021-03-26 12:41:28 +0100 (Fri, 26 Mar 2021) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_main_reportfig.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m
A       cat_surf_renderv.m

(1) Fixed:    Removed multiple tiny bugs.
(2) Changed:  Lightly optimized deformation parameter in cat_surf_createCS2.
(3) New:      Added simple surface renderer cat_surf_renderv as backup for cases
              without openGL and updated cat_main_reportfig.


------------------------------------------------------------------------
r1786 | gaser | 2021-03-24 22:08:28 +0100 (Wed, 24 Mar 2021) | 15 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_io_colormaps.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_APRG.m
M       cat_main_correctmyelination.m

(1) Changed: Parameters restype and resval from cat_defaults are now added as
             selection in cat_conf_extopts.m which were previously hard-coded.
(2) Changed: Updated help text.


------------------------------------------------------------------------
r1785 | gaser | 2021-03-22 22:53:43 +0100 (Mon, 22 Mar 2021) | 33 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_defaults.m
A       cat_io_data2mat.m
M       cat_main_reportstr.m
A       cat_plot_cov.m
M       cat_run_job1639.m
M       cat_stat_check_cov.m
M       cat_stat_spm2x.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_ui.m
A       templates_MNI152NLin2009cAsym/mTemplate_T1.nii

(1) Added:   New function for plotting rotated covariance/correlation matrix
             (cat_plot_cov.m).
(2) Added:   New function for saving spatially registered volume or resampled
             surface data as Matlab data matrix for further use with machine
             learning tools (cat_io_data2mat.m).
(3) Added:   Added masked T1 template for overlay.
(4) Changed: Updated example overlays in cat_vol_slice_overlay_ui.m.
(5) Changed: Updated cat_stat_check_cov.m to consider use of new function
             cat_plot_cov.m.
(6) Changed: Default T1 image for overlay in cat_defaults.m is now a masked
             image.
(7) Changed: Added configs for new cat_io_data2mat function and renamed mayn sub-
             functions in cat_conf_tools.m.
(8) Changed: Updated help text.
(9) Fixed:   Added check whether extopts.SRP is defined in cat_main_reportstr.m.
(10)Fixed:   Got finally rid of colored border if colorbar was added in
             cat_vol_slice_overlay.m

------------------------------------------------------------------------
r1784 | dahnke | 2021-03-22 08:37:04 +0100 (Mon, 22 Mar 2021) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main_reportfig.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m

(1) Fixed:    Removed multiple tiny bugs.

------------------------------------------------------------------------
r1783 | dahnke | 2021-03-21 10:22:25 +0100 (Sun, 21 Mar 2021) | 29 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_long.m
M       cat_long_main.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_correctmyelination.m
M       cat_main_registration.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m

(1) Fixed:    Corrected bug in longitudinal surface processing in cat_surf_createCS2.
(2) Changed:  Corrected tiny (command line output) bugs in cat_conf_extopts,
              cat_main_correctmyelination, cat_main_registration, cat_main_reportstr,
              cat_main_reportfig, cat_main_updateSPM(1639), cat_run_job(1639),
              cat_surf_createCS(2), cat_surf_fun.
(3) Changed:  Removed new_realease setting from LAS myelination correction blocks in
              cat_main(1639).
(4) Changed:  Updated BB field in cat_conf_long and cat_long_main.


------------------------------------------------------------------------
r1782 | dahnke | 2021-03-18 18:50:42 +0100 (Thu, 18 Mar 2021) | 26 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_reportstr.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_display.m
M       cat_surf_fun.m
M       cat_vol_pbt.m
!       templates_surfaces/lh.central.freesurfer.gii
!       templates_surfaces/lh.sphere.freesurfer.gii
!       templates_surfaces/rh.central.freesurfer.gii
!       templates_surfaces/rh.sphere.freesurfer.gii

(1) Changed:   Renamed extopts.collcorr parameter to extopts.SRP and
               updated options and help in cat_conf_extopts, cat_defaults,
               cat_main(1639), cat_surf_createCS(2),
(2) Changed:   Updated self-intersection corrections in cat_surf_fun.
(3) Changed:   Enhanced range of Ypp to support reconstruction of white and
               pial surfaces.
(4) Changed:   Added thickness/pbt settings in cat_surf_display.


------------------------------------------------------------------------
r1781 | gaser | 2021-03-15 23:01:33 +0100 (Mon, 15 Mar 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_main_reportfig.m
M       cat_surf_fun.m

(1) Changed: Corrected estimation of window size in cat_main_reportfig.m if
             units are "normalized" in new spm12 version.
(2) Changed: Corrected 2nd argument for calls of spm_mesh_area to consider
             new SPM12 version.


------------------------------------------------------------------------
r1780 | gaser | 2021-03-15 15:56:14 +0100 (Mon, 15 Mar 2021) | 23 lines

Changed paths:
M       CHANGES.txt
M       cat_main1639.m
M       cat_main_updateSPM1639.m
M       cat_run.m
M       cat_run_job1639.m
M       cat_spm_results_ui.m
M       cat_stat_spm.m
M       cat_surf_createCS.m
M       cat_vol_defs.m
M       cat_vol_groupwise_ls.m
M       html/cat_methods_RBM.html
 M      templates_surfaces/cb.central.Template_T1.gii
 M      templates_surfaces/cb.thickness.Template_T1

(1) Changed: Added check in cat_stat_spm.m to ensure that template exists.
(2) Changed: Adapted code for categorical interpolation in cat_vol_defs.m
             w.r.t. new SPM12 version.
(3) Fixed:   Added field check for SPM.xVol.G in cat_spm_results_ui.m
(4) Fixed:   Links to T1 and brainmask in cat_vol_groupwise_ls.m were wrong.
(5) Fixed:   Corrected wrong name for HCP meshes in cat_methods_RBM.html.
(6) Fixed:   Corrected typos...

------------------------------------------------------------------------
r1779 | dahnke | 2021-03-11 19:39:36 +0100 (Thu, 11 Mar 2021) | 42 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_io_colormaps.m
M       cat_long_main.m
M       cat_main1639.m
M       cat_main_LAS2.m
M       cat_main_LAS21639.m
M       cat_main_correctmyelination.m
M       cat_main_registration.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_main_write.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m
M       cat_surf_render2.m
M       cat_vol_partvol.m
M       cat_vol_partvol1639.m
!       templates_surfaces_32k/lh.central.freesurfer.gii
!       templates_surfaces_32k/lh.sphere.freesurfer.gii
!       templates_surfaces_32k/rh.central.freesurfer.gii
!       templates_surfaces_32k/rh.sphere.freesurfer.gii

(1) Changed:   Updated boundary box setting.
(2) New:       Added turbo colormap in cat_io_colormaps.
(3) New:       Added turbo colormap in cat_surf_render2.
(4) Fixed:     Corrected some bugs in cat_surf_render2.
(5) Fixed:     Corrected BB settings in cat_main(1639) and cat_main_registration.
(6) Fixed:     Added cat_vol_sample function to call spm_sample_vol
               for different BBs and replace old calls in
               cat_main_correctmyelination, cat_main_LAS2(1639), cat_main_write,
               cat_main_updateSPM(1639), cat_vol_partvol(1639).
(7) Changed:   Small corrections in cat_surf_createCS and cat_surf_fun.
(8) Fixed:     Many corrections in cat_surf_createCS2.



------------------------------------------------------------------------
r1778 | dahnke | 2021-03-06 17:02:24 +0100 (Sat, 06 Mar 2021) | 36 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_long.m
M       cat_defaults.m
M       cat_long_createTPM.m
M       cat_long_main.m
M       cat_main1639.m
M       cat_main_LAS21639.m
M       cat_main_correctmyelination.m
M       cat_main_registration.m
M       cat_main_updateSPM1639.m
M       cat_main_write.m
M       cat_run_job1639.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_vol_groupwise_ls.m

(1)  New:      Added high background detection in cat_run_job1639.
(2)  New:      Added BB in cat_conf_long, cat_long_main, cat_conf_extopts and
               cat_vol_groupwise_ls.
(3)  New:      Added correction of self-intersections in cat_surf_createCS
               and GUI options in cat_conf_extopts.
(4)  Fixed:    Corrected affine registration settings in cat_run_job1639.
(5)  Fixed:    Changed smoothing and background settings of head tissue
               classes in cat_long_createTPM.
(6)  Fixed:    Improved background definition in affine/rigid export in
               cat_main_write.
(7)  Fixed:    Corrected bug in case of TPM BB in cat_main_registration.
(8)  Fixed:    Small corrections in cat_main_correctmyelination.
(9)  Fixed:    Added resval value in cat_defaults?
(10) Changes:  Small correction to avoid call of test functions in
               cat_surf_createCS(2).



------------------------------------------------------------------------
r1777 | gaser | 2021-03-05 16:25:00 +0100 (Fri, 05 Mar 2021) | 21 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_long_createTPM.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_surf_createCS2.m
M       cat_surf_render.m
M       cat_surf_vol2surf.m
M       html/cat.html
MM      templates_surfaces/mesh.central.Template_T1.gii
MM      templates_surfaces_32k/mesh.central.Template_T1.gii

(1) Chamged: Disable setCOM for useprior in cat_run_job1649.m and cat_run_job.m.
(2) Changed: Try to replace path of undrlying surface to cat12 and correct
             template name to new template in cat_surf_render.m.
(3) Changed: Removed unnecessary warning in cat_long_createTPM.m if template
             size  differs.
(4) Changed: Suppress some outputs depending on verbose level and useprior flag.
(3) Fixed:   Added missing bracket in cat_surf_vol2surf.m that caused crash.

------------------------------------------------------------------------
r1776 | gaser | 2021-02-28 15:00:49 +0100 (Sun, 28 Feb 2021) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main1639.m
M       cat_main_LAS.m
M       cat_main_LAS2.m
M       cat_main_LAS21639.m
M       cat_main_reportstr.m
M       html/cat_versions.html
 M      templates_MNI152NLin2009cAsym/cat_1mm.nii
A       templates_surfaces/cb.central.Template_T1.gii
A       templates_surfaces/cb.thickness.Template_T1

(1) Chamged: Changed list of default options for internal interpolation because
             "native" seems to better more appropriate than "best native".
(2) Changed: Updated version information.
(3) Changed: Updated LAS formatted output for command line report.

------------------------------------------------------------------------
r1775 | gaser | 2021-02-27 21:08:33 +0100 (Sat, 27 Feb 2021) | 35 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_cat.m
M       cat_conf_extopts.m
M       cat_long_multi_run.m
M       cat_surf_createCS2.m
M       cat_surf_gyrification.m
M       spm_cat12.m
M       standalone/cat_standalone.sh
D       templates_surfaces/lc.central.freesurfer.gii
D       templates_surfaces/lc.sphere.freesurfer.gii
M       templates_surfaces/lh.central.Template_T1.gii
M       templates_surfaces/lh.thickness.Template_T1
M       templates_surfaces/mesh.central.Template_T1.gii
D       templates_surfaces/rc.central.freesurfer.gii
D       templates_surfaces/rc.sphere.freesurfer.gii
M       templates_surfaces/rh.central.Template_T1.gii
M       templates_surfaces/rh.thickness.Template_T1
M       templates_surfaces/templates_surfaces.man
M       templates_surfaces_32k/lh.central.Template_T1.gii
M       templates_surfaces_32k/lh.thickness.Template_T1
M       templates_surfaces_32k/mesh.central.Template_T1.gii
M       templates_surfaces_32k/rh.central.Template_T1.gii
M       templates_surfaces_32k/rh.thickness.Template_T1
M       templates_surfaces_32k/templates_surfaces_32k.man

(1) Chamged: Updated Template_T1 surfaces and thickness values using
             collcorr=24.
(2) Changed: Removed old cerebellar surfaces in templates_surfaces.
(3) Changed: Updated template descriptions in templates_surfaces*.
(4) Changed: Updatd help text for cat_standalone.sh.
(5) Changed: Added "vox" to fields that should be removed in cat_batch_cat
             to suppress warnings.
(6) Fixed:   Added check for extopts.vox field in cat_long_multi_run.m.

------------------------------------------------------------------------
r1774 | gaser | 2021-02-27 00:51:11 +0100 (Sat, 27 Feb 2021) | 21 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_results.m
M       cat_surf_vol2surf.m
M       cat_vol_ROI_summarize.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_ui.m
M       check_pipeline/batch_surface_pipeline.m
M       check_pipeline/batch_volume_pipeline.m
D       templates_MNI152NLin2009cAsym/TPM.nii

(1) Chamged: Added check for bounding box to ensure that new template is not
             used for overlaying results or mapping volumes to surfaces with
             old data from previous versions that are not compatible anymore.
(2) Fixed:   Added conversion to char for checking for extopts.shootingT1.




------------------------------------------------------------------------
r1773 | gaser | 2021-02-26 22:51:15 +0100 (Fri, 26 Feb 2021) | 153 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cat12.m
M       cat_batch_cat.m
M       cat_conf_catsimple.m
M       cat_conf_extopts.m
M       cat_conf_output.m
M       cat_defaults.m
M       cat_long_main.m
M       cat_main_LAS.m
M       cat_main_LAS2.m
M       cat_main_LAS21639.m
MM      cat_main_correctmyelination.m
M       cat_main_reportstr.m
M       cat_run.m
D       cat_run1173
D       cat_run1173/cat_conf_ROI1173.m
D       cat_run1173/cat_conf_extopts1173.m
D       cat_run1173/cat_conf_long1173.m
D       cat_run1173/cat_conf_opts1173.m
D       cat_run1173/cat_defaults1173.m
D       cat_run1173/cat_get_defaults1173.m
D       cat_run1173/cat_long_main1173.m
D       cat_run1173/cat_long_multi_run1173.m
D       cat_run1173/cat_main1173.m
D       cat_run1173/cat_main_LAS1173.m
D       cat_run1173/cat_main_gcut1173.m
D       cat_run1173/cat_main_registration1173.m
D       cat_run1173/cat_run1173.m
D       cat_run1173/cat_run_job10701173.m
D       cat_run1173/cat_run_job1173.m
D       cat_run1173/cat_run_job_APP_SPM1173.m
D       cat_run1173/cat_run_job_APP_final.m
D       cat_run1173/cat_run_job_APP_init10701173.m
D       cat_run1173/cat_run_newcatch1173.m
D       cat_run1173/cat_surf_createCS1173.m
D       cat_run1173/cat_tst_qa1173.m
D       cat_run1173/cat_vol_isarnlm.m
D       cat_run1173/cat_vol_partvol1173.m
D       cat_run1173/cat_vol_sanlm1173.m
D       cat_run1173plus
D       cat_run1173plus/cat_conf_extopts1173plus.m
D       cat_run1173plus/cat_conf_long1173plus.m
D       cat_run1173plus/cat_conf_opts1173plus.m
D       cat_run1173plus/cat_defaults1173plus.m
D       cat_run1173plus/cat_get_defaults1173plus.m
D       cat_run1173plus/cat_main1173plus.m
D       cat_run1173plus/cat_run1173plus.m
D       cat_run1173plus/cat_run_job10701173plus.m
D       cat_run1173plus/cat_run_job1173plus.m
D       cat_run1173plus/cat_run_newcatch1173plus.m
D       cat_run1445
D       cat_run1445/cat_conf_ROI1445.m
D       cat_run1445/cat_conf_extopts1445.m
D       cat_run1445/cat_conf_long1445.m
D       cat_run1445/cat_conf_opts1445.m
D       cat_run1445/cat_defaults1445.m
D       cat_run1445/cat_get_defaults1445.m
D       cat_run1445/cat_long_main1445.m
D       cat_run1445/cat_long_multi_run1445.m
D       cat_run1445/cat_main1445.m
D       cat_run1445/cat_main_LAS1445.m
D       cat_run1445/cat_main_gcut1445.m
D       cat_run1445/cat_main_registration1445.m
D       cat_run1445/cat_run1445.m
D       cat_run1445/cat_run_job10701445.m
D       cat_run1445/cat_run_job1445.m
D       cat_run1445/cat_run_job_APP_init10701445.m
D       cat_run1445/cat_run_newcatch1445.m
D       cat_run1445/cat_surf_createCS1445.m
D       cat_run1445/cat_vol_partvol1445.m
D       cat_run1445/cat_vol_sanlm1445.m
D       cat_run1585
D       cat_run1585/cat_conf_ROI1585.m
D       cat_run1585/cat_conf_extopts1585.m
D       cat_run1585/cat_conf_long1585.m
D       cat_run1585/cat_conf_opts1585.m
D       cat_run1585/cat_defaults1585.m
D       cat_run1585/cat_get_defaults1585.m
D       cat_run1585/cat_main1585.m
D       cat_run1585/cat_main_APRG1585.m
D       cat_run1585/cat_main_LAS1585.m
D       cat_run1585/cat_main_amap1585.m
D       cat_run1585/cat_main_kamap1585.m
D       cat_run1585/cat_main_registration1585.m
D       cat_run1585/cat_main_updateSPM1585.m
D       cat_run1585/cat_main_updateWMHs1585.m
D       cat_run1585/cat_run1585.m
D       cat_run1585/cat_run_job10701585.m
D       cat_run1585/cat_run_job1585.m
D       cat_run1585/cat_run_job_APP_SPMfinal1585.m
D       cat_run1585/cat_run_job_APP_SPMinit1585.m
D       cat_run1585/cat_run_job_APP_final1585.m
D       cat_run1585/cat_run_job_APP_init10701585.m
D       cat_run1585/cat_run_job_APP_init1585.m
D       cat_run1585/cat_run_job_APRGs1585.m
D       cat_run1585/cat_run_newcatch1585.m
D       cat_run1585/cat_surf_createCS1585.m
D       cat_run1585/cat_surf_createCS21585.m
D       cat_run1585/cat_vol_approx1585.m
D       cat_run1585/cat_vol_pbt1585.m
D       cat_run_job1070.m
M       cat_run_newcatch.m
M       cat_simple.m
M       cat_surf_createCS2.m
M       cat_surf_info.m
M       cat_vol_ROI_summarize.m
M       standalone/cat_standalone_segment.txt
M       standalone/cat_standalone_segment_long.txt
M       standalone/cat_standalone_simple.txt
M       tbx_cfg_cat.m
A       templates_MNI152NLin2009cAsym/cat_1mm.nii
D       templates_surfaces/lc.central.Template_T1_IXI555_MNI152_GS.gii
D       templates_surfaces/lc.thickness.Template_T1_IXI555_MNI152_GS
M       templates_surfaces/lh.central.Template_T1.gii
D       templates_surfaces/lh.central.Template_T1_IXI555_MNI152_GS.gii
M       templates_surfaces/lh.thickness.Template_T1
D       templates_surfaces/lh.thickness.Template_T1_IXI555_MNI152_GS
A       templates_surfaces/mesh.central.Template_T1.gii
D       templates_surfaces/mesh.central.Template_T1_IXI555_MNI152_GS.gii
D       templates_surfaces/rc.central.Template_T1_IXI555_MNI152_GS.gii
D       templates_surfaces/rc.thickness.Template_T1_IXI555_MNI152_GS
M       templates_surfaces/rh.central.Template_T1.gii
D       templates_surfaces/rh.central.Template_T1_IXI555_MNI152_GS.gii
M       templates_surfaces/rh.thickness.Template_T1
D       templates_surfaces/rh.thickness.Template_T1_IXI555_MNI152_GS
M       templates_surfaces_32k/lh.central.Template_T1.gii
D       templates_surfaces_32k/lh.central.Template_T1_IXI555_MNI152_GS.gii
M       templates_surfaces_32k/lh.thickness.Template_T1
D       templates_surfaces_32k/lh.thickness.Template_T1_IXI555_MNI152_GS
A       templates_surfaces_32k/mesh.central.Template_T1.gii
D       templates_surfaces_32k/mesh.central.Template_T1_IXI555_MNI152_GS.gii
M       templates_surfaces_32k/rh.central.Template_T1.gii
D       templates_surfaces_32k/rh.central.Template_T1_IXI555_MNI152_GS.gii
M       templates_surfaces_32k/rh.thickness.Template_T1
D       templates_surfaces_32k/rh.thickness.Template_T1_IXI555_MNI152_GS

(1) Changed: Changed CAT12 to new template and talas space MNI152NLin2009cAsym.
(2) Chamged: Removed old templates_volumes folder.
(3) Changed: Changed defaults to WMHC=2 to always correct WMHs to WM.
(4) Changed: Removed folders with previous versions that arenot supported
             anymore.
(5) Changed: Updated standalone and catc_batch_* scripts to consider new
             changes.
(6) Changed: Removed cat_run_job1070.m that was only needed for ancient Matlab
             versions.
(7) Fixed:   Corrected typo in cat_vol_ROI_summarize.m that caused errors.
(8) Fixed:   Removed call of Vyp0s in cat_surf_createCS2.m that was not
             existing.
(9) Fixed:   Corrected wrong definitions for interpolations in
             cat_conf_extopts.m

------------------------------------------------------------------------
r1772 | gaser | 2021-02-26 00:41:54 +0100 (Fri, 26 Feb 2021) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_updateSPM1639.m
M       cat_run.m

(1) Changed: Added changes that were removed with last release.
(2) Chamged: Removed extopts.resval from cat_defaults because it was only
             recognized in expert mode.
(3) Changed: Changed resval to [1 0.3] for optimal interpolation to prevent
             unnecessary interpolytion.
(4) Fixed:   Paths of T1 and brainmask were corrected in cat_defaults.m.


------------------------------------------------------------------------
r1771 | dahnke | 2021-02-25 17:27:50 +0100 (Thu, 25 Feb 2021) | 29 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main.m
M       cat_main1639.m
A       cat_main_correctmyelination.m
M       cat_main_gintnormi.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_run_job1639.m
M       cat_surf_createCS.m
M       cat_vol_partvol.m
M       cat_vol_partvol1639.m
M       cat_vol_resize.m

(1) New:      Added line- and box-plot in thickness histogram to allow more
              details on the second view.
(2) Fixed:    Corrected developer report kmeans thickness value that now shows
              the largest peak.
(3) Fixed:    Adapted WMHCstr by voxel size in cat_vol_partvol[1639] to reduce
              overcorrections in problematic data.
(4) Fixed:    Corrected output of white/pial preview surfaces.
(5) Fixed:    Corrected thickness output values to final FS and not PBT metric.
(6) New:      Added new correction for myelination differences for LAS, which
              still needs further testing and refinements.


------------------------------------------------------------------------
r1770 | gaser | 2021-02-25 16:34:26 +0100 (Thu, 25 Feb 2021) | 48 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Contents_info.txt
M       cat_conf_ROI.m
M       cat_conf_output.m
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_install_atlases.m
M       cat_io_checkdepfiles.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_registration.m
M       cat_main_registration2.m
M       cat_roi_roi2surf.m
M       cat_run.m
M       cat_simple.m
M       cat_spm_results_ui.m
M       cat_stat_analyze_ROIs.m
M       cat_stat_spm.m
M       cat_surf_display.m
M       cat_surf_info.m
M       cat_surf_render.m
M       cat_surf_render2.m
M       cat_surf_results.m
M       cat_surf_surf2roi.m
M       cat_surf_vol2surf.m
M       cat_tst_cattest.m
M       cat_update.m
M       cat_vol_ROI_summarize.m
M       cat_vol_groupwise_ls.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_rgb_ui.m
M       cat_vol_slice_overlay_ui.m
M       check_pipeline/batch_volume_pipeline.m
M       html/cat.html
M       html/cat.txt
M       html/cat_methods_RBM.html
M       html/cat_versions.html
M       templates_MNI152NLin2009cAsym/T1.nii
M       templates_MNI152NLin2009cAsym/TPM_Age11.5.nii
M       templates_MNI152NLin2009cAsym/brainmask.nii
M       templates_surfaces/templates_surfaces.man
M       templates_surfaces_32k/templates_surfaces_32k.man

Changed: Prepared all functions for use with the new template by using defined
         names in cat_defaults.

------------------------------------------------------------------------
r1769 | gaser | 2021-02-23 21:03:33 +0100 (Tue, 23 Feb 2021) | 32 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_ROI.m
M       cat_conf_extopts.m
M       cat_conf_tools.m
M       cat_io_report.m
M       cat_long_biascorr.m
M       cat_long_createTPM.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_amap.m
M       cat_main_registration.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_run_newcatch.m
M       cat_spm_results_ui.m
M       cat_surf_createCS2.m
M       cat_surf_info.m
M       cat_vol_imcalc.m
M       cat_vol_pbt.m
M       cat_vol_pbt2.m

(1) Changed: Updated help text.
(2) Changed: Updated cat_long_createTPM.m to allow loading of TPMs with
             different bounding box and voxel size.
(3) Fixed:   Updated cat_surf_info to correctly obtain underlying surface for
             analysis data.
(4) Fixed:   Use of SPM12 segmentation for surface extraction is now again
             working.
(5) Fixed:   Corrected many typos.


------------------------------------------------------------------------
r1768 | gaser | 2021-02-18 01:24:32 +0100 (Thu, 18 Feb 2021) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_io_xml.m
M       cat_long_createTPM.m
M       cat_long_main.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_updateSPM1639.m
M       html/cat.html

(1) Fixed: Corrected many typos.
(2) Fixed: Added check whether file exists for deleting surface preview.

------------------------------------------------------------------------
r1767 | gaser | 2021-02-14 23:40:42 +0100 (Sun, 14 Feb 2021) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_main_gintnormi.m
M       cat_run_job1639.m
M       html/cat.html

(1) Changed: Set affine regularization in cat_run_job1639.m back to 'subj'.
(2) Changed: Force to use old threshold estimation strategy in
             cat_main_gintnormi.m.

------------------------------------------------------------------------
r1766 | dahnke | 2021-02-12 12:42:56 +0100 (Fri, 12 Feb 2021) | 27 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_gintnormi.m
M       cat_main_registration.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_run.m
M       cat_run_job1639.m
M       cat_surf_createCS.m

(1) Changed:  Set new report as default for all users.
(2) Fixed:    Corrected lesion settings in cat_run_job#.
(3) Fixed:    Corrected settings for boundary box.
(4) Fixed:    Corrected problem with missing trans variable.
(5) Fixed:    Corrected bug in intensity scaling.
(5) Changed:  Remove BB parameter from cat_default and expert GUI and udated BB settings.
(6) Changed:  Added function to improve the input image by the SPM segmentation
              to stabilize problematic dataset (in development).
(7) Changed:  Added some volumetric values of the SPM segmentation to the XML.


------------------------------------------------------------------------
r1765 | gaser | 2021-02-12 01:32:27 +0100 (Fri, 12 Feb 2021) | 18 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cat_conf_tools.m
M       cat_vol_createMPM.m
M       templates_MNI152NLin2009cAsym/cobra.nii
M       templates_MNI152NLin2009cAsym/cobra.txt
M       templates_MNI152NLin2009cAsym/ibsr.nii
M       templates_MNI152NLin2009cAsym/ibsr.txt
M       templates_MNI152NLin2009cAsym/lpba40.nii
M       templates_MNI152NLin2009cAsym/lpba40.txt

(1) Changed: Undone last changes for cat_vol_create_MPM.m which were not
             meaningful.
(2) Changed: Added some more cleaning and permission commands to Makefile to
             clean up distributions before zipping.
(3) Changed: Updated remaining atlases in templates_MNI152NLin2009cAsym.

------------------------------------------------------------------------
r1764 | gaser | 2021-02-11 11:15:51 +0100 (Thu, 11 Feb 2021) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_createMPM.m

Changed: Updated cat_vol_createMPM.m to preserve all label values even if some
         are below defined threshold.

------------------------------------------------------------------------
r1763 | gaser | 2021-02-11 09:27:45 +0100 (Thu, 11 Feb 2021) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
RM      cat_vol_ROI_summarize.m
M       html/cat.html

Changed: Updated help text.

------------------------------------------------------------------------
r1762 | gaser | 2021-02-11 01:14:55 +0100 (Thu, 11 Feb 2021) | 12 lines

Changed paths:
M       CHANGES.txt
MM      cat_vol_ROI_summarize.m
M       development/Template_0_GS1mm.nii
M       development/Template_1_GS1mm.nii
M       development/Template_2_GS1mm.nii
M       development/Template_3_GS1mm.nii
M       development/Template_4_GS1mm.nii

Changed: Updated 1mm GS-Templates in development folder to new bounding box.


------------------------------------------------------------------------
r1761 | gaser | 2021-02-11 00:47:37 +0100 (Thu, 11 Feb 2021) | 44 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_output.m
M       cat_io_writenii.m
M       cat_main_reportfig.m
M       cat_main_write.m
M       cat_vol_set_com.m
M       templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii
M       templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii
M       templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii
M       templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii
M       templates_MNI152NLin2009cAsym/Template_0_GS.nii
M       templates_MNI152NLin2009cAsym/Template_1_Dartel.nii
M       templates_MNI152NLin2009cAsym/Template_1_GS.nii
M       templates_MNI152NLin2009cAsym/Template_2_Dartel.nii
M       templates_MNI152NLin2009cAsym/Template_2_GS.nii
M       templates_MNI152NLin2009cAsym/Template_3_Dartel.nii
M       templates_MNI152NLin2009cAsym/Template_3_GS.nii
M       templates_MNI152NLin2009cAsym/Template_4_Dartel.nii
M       templates_MNI152NLin2009cAsym/Template_4_GS.nii
M       templates_MNI152NLin2009cAsym/Template_5_Dartel.nii
M       templates_MNI152NLin2009cAsym/Template_6_Dartel.nii
M       templates_MNI152NLin2009cAsym/aal3.nii
M       templates_MNI152NLin2009cAsym/brainmask.nii
M       templates_MNI152NLin2009cAsym/cat.nii
M       templates_MNI152NLin2009cAsym/cat_strokelesions_ATLAS303.nii
M       templates_MNI152NLin2009cAsym/cat_wmh.nii
M       templates_MNI152NLin2009cAsym/cat_wmh_miccai2017.nii
M       templates_MNI152NLin2009cAsym/hammers.nii
M       templates_MNI152NLin2009cAsym/mori.nii
M       templates_MNI152NLin2009cAsym/neuromorphometrics.nii
M       templates_external/y_IXI555Dartel_to_MNI152NLin2009cAsym.nii
M       templates_external/y_MNI152NLin6Asym_to_MNI152NLin2009cAsym.nii
M       templates_external/y_MNIColin27_to_MNI152NLin2009cAsym.nii

(1) Changed: Updated Templates and atlases in templates_MNI152NLin2009cAsym
             with new bounding box.
(2) Changed: Set output in report to new surface display with multiple views.
(3) Fixed:   Corrected some typos
(4) Fixed:   Corrected field name for spatial registration in cat_conf_extopts.m
(5) Fixed:   Added spaces between strings to descrip-field for saving normalized
             images.

------------------------------------------------------------------------
r1760 | gaser | 2021-02-10 10:48:13 +0100 (Wed, 10 Feb 2021) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main_registration.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_stat_kmeans.m
A       cat_vol_ROI_summarize.m
M       html/cat.html

(1) Fixed: Corrected help text in cat_conf_extopts.m that caused errors.
(2) Fixed: Corected typos in help text.

------------------------------------------------------------------------
r1759 | dahnke | 2021-02-09 14:31:22 +0100 (Tue, 09 Feb 2021) | 29 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_gintnorm1639.m
M       cat_main_kamap.m
M       cat_main_registration.m
M       cat_main_reportstr.m
M       cat_main_roi.m
M       cat_main_updateSPM.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_stat_kmeans.m

(1) New:      Heavy update of cat_main_registration:
              Implemented boundary box (BB) to control normalized output.
              Updated handling of large ventricles for the optimized shooting.
              Corrected bug in the resizing-matrix in cat_main_registration.
              Additional GUI variables in cat_conf_extopts and cat_defaults.
              Corrected stroke lesion correction/handling/display.
              Related small corrections in cat_main_roi.
(2) Deleted:  Removed cat_main_registration2 and calls in cat_main# that are
              now obsolete.
(3) Fixed:    Corrected bug in percentage class definition in cat_stat_kmeans.


------------------------------------------------------------------------
r1758 | gaser | 2021-02-05 00:26:47 +0100 (Fri, 05 Feb 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_surf_results.m
M       cat_vol_slice_overlay_ui.m
 M      templates_surfaces/mesh.central.Template_T1_IXI555_MNI152_GS.gii
 M      templates_surfaces_32k/mesh.central.Template_T1_IXI555_MNI152_GS.gii

Fixed: Log-p scaled threshold for P<0.05 was slightly uncorrect.


------------------------------------------------------------------------
r1757 | gaser | 2021-02-05 00:12:18 +0100 (Fri, 05 Feb 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_stat_spm2x.m
M       cat_surf_results.m

(1) Fixed: Log-p scaled threshold for P<0.05 was slightly uncorrect.
(2) Fixed: Thresholding the results in cat_surf_results.m was slightly
           uncorrect. Thanks to Pravesh Parekh for pointing to that error.


------------------------------------------------------------------------
r1756 | gaser | 2021-02-04 22:23:11 +0100 (Thu, 04 Feb 2021) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_createMPM.m
M       templates_MNI152NLin2009cAsym/ibsr.nii
M       templates_MNI152NLin2009cAsym/lpba40.nii
A       templates_surfaces/mesh.central.Template_T1_IXI555_MNI152_GS.gii
A       templates_surfaces_32k/mesh.central.Template_T1_IXI555_MNI152_GS.gii

(1) Added:   Added again mesh.central.Template_T1_IXI555_MNI152_GS.gii which
             is necessary for displaying results.
(2) Changed: Updated output format for cat_vol_createMPM.m.

------------------------------------------------------------------------
r1755 | gaser | 2021-02-04 21:29:16 +0100 (Thu, 04 Feb 2021) | 19 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_conf_ROI.m
M       cat_conf_extopts.m
M       cat_conf_stools.m
MM      cat_main_update_intnorm.m
M       cat_surf_fun.m
M       cat_surf_surf2roi.m
 M      html/cat_methods_affreg.html
 M      templates_surfaces/lh.thickness.Template_T1
 M      templates_surfaces/rh.thickness.Template_T1
 M      templates_surfaces_32k/lh.thickness.Template_T1
 M      templates_surfaces_32k/rh.thickness.Template_T1

(1) Changed: Updated help text.
(2) Changed: Updated CAT12 manual.


------------------------------------------------------------------------
r1754 | gaser | 2021-02-03 19:03:44 +0100 (Wed, 03 Feb 2021) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_ROI.m
M       cat_main_reportfig.m

(1) Fixed:   Atlases in cat_vol_ROI_summarize batch were not correctly
             recognized if only defined in expert mode.
(2) Changed: Switch off some annoying warnings in cat_main_reportfig.m


------------------------------------------------------------------------
r1753 | gaser | 2021-02-03 18:15:39 +0100 (Wed, 03 Feb 2021) | 46 lines

Changed paths:
M       Amap.c
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_ROI.m
M       cat_conf_tools.m
D       cat_io_3Dto4D.m
        > moved to development/cat_io_3Dto4D.m
M       cat_spm_preproc_write8.m
M       cat_surf_results.m
M       cat_vol_ROIval.c
M       cat_vol_createMPM.m
M       cat_vol_defs.m
M       cat_vol_series_align.m
M       development/Template_0_GS1mm.nii
M       development/Template_1_GS1mm.nii
M       development/Template_2_GS1mm.nii
M       development/Template_3_GS1mm.nii
M       development/Template_4_GS1mm.nii
A  +    development/cat_io_3Dto4D.m
        > moved from cat_io_3Dto4D.m
M       html/cat.html
M       templates_MNI152NLin2009cAsym/Template_1_Dartel.nii
M       templates_MNI152NLin2009cAsym/Template_2_Dartel.nii
M       templates_MNI152NLin2009cAsym/Template_3_Dartel.nii
M       templates_MNI152NLin2009cAsym/Template_4_Dartel.nii
M       templates_MNI152NLin2009cAsym/Template_5_Dartel.nii
M       templates_MNI152NLin2009cAsym/Template_6_Dartel.nii
 M      templates_surfaces/lh.central.Template_T1.gii
 M      templates_surfaces/rh.central.Template_T1.gii
 M      templates_surfaces_32k/lh.central.Template_T1.gii
 M      templates_surfaces_32k/rh.central.Template_T1.gii
 M      templates_volumes/anatomy3.csv
 M      templates_volumes/anatomy3.nii
MM      templates_volumes/anatomy3.txt

(1) Changed: Updated cat_vol_ROI_summarize.m
(2) Changed: Added batch to call cat_vol_ROI_summarize from GUI.
(3) Changed: Function cat_vol_defs now allows to return deformed image without
             saving it.
(4) Changed: Added threshold option to cat_vol_create_MPM.m.
(5) Changed: Added option to use cutomized colormaps to cat_surf_results.m.
(6) Changed: Moved cat_io_3Dto4D.m to development folder
(7) Changed: Updated help text and made some cosmetic changes to code.

------------------------------------------------------------------------
r1752 | dahnke | 2021-01-28 16:52:32 +0100 (Thu, 28 Jan 2021) | 57 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_io_addwarning.m
M       cat_io_colormaps.m
M       cat_io_report.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_LAS2.m
M       cat_main_amap.m
M       cat_main_amap1639.m
M       cat_main_gintnorm.m
M       cat_main_gintnormi.m
M       cat_main_registration.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
A       cat_main_update_intnorm.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_run_newcatch.m
M       cat_stat_kmeans.m
M       cat_surf_display.m
M       cat_vol_partvol.m
M       cat_vol_resize.m
M       html/cat_methods_WMHC.html
A       html/cat_methods_affreg.html
M       html/cat_methods_warnings.html
M       html/style.css

(1)  Changed:    Updated CAT report layout in cat_main_reportfig (default report).
(2)  Fixed:      Corrected multiple bugs in the current pipeline. Corrected errors in
                 ignoreError setting in cat_main_amap and cat_vol_partvol.
                 Small correction to make cat_main_gintnorm more similar to
                 cat_main_gintnorm1639 in the T1 processing.
(3)  Changed:    Deactivaded affreg in case of high intensity background in cat_run_job
                 to focus on maffreg that works faster and better because the T1 template
                 does not fit to the MP2Rage.
(4)  Fixed:      Corrected some issues in the MP2rage processing in cat_main_gintnorm but
                 further work is required.
(5)  Changed:    Extended setCOM parameter for experts in cat_conf_extopts to
                 include the different affine registration strategies.
(6)  New:        Added affmod parameter for final adaption of the affine registration in
                 cat_conf_extopts, cat_run, cat_run_job[1639], and cat_main_reportsstr.
(7)  Fixed:      Small correction in cat_io_report (error report).
(8)  Fixed:      Remove double entry that delete preview data in cat_main(1639).
(9)  Fixed:      Removed double warning for new pipeline in cat_run_newcatch.
(10) New:        Added function for intensity scaling that can be used by setting
                 extopts.new_release to 1 that could also be used to use the AMAP
                 thresholds for final intensity scaling (prepared but not working yet).
(11) Changed:    Added interpolation to improve intensity normalization in
                 cat_main_gintnormi.
(12) Fixed:      Corrected small bug in cat_vol_resize.
(13) Fixed:      Corrected tiny bug in cat_stat_kmeans.


------------------------------------------------------------------------
r1751 | gaser | 2021-01-12 07:58:54 +0100 (Tue, 12 Jan 2021) | 80 lines

Changed paths:
M       CHANGES.txt
 M      development/JulichBrain2CAT12.m
 M      development/Template_0_GS1mm.nii
 M      development/Template_1_GS1mm.nii
 M      development/Template_2_GS1mm.nii
 M      development/Template_3_GS1mm.nii
 M      development/Template_4_GS1mm.nii
 M      development/correct_tpm2one.m
 M      templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.csv
 M      templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii
 M      templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.csv
 M      templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii
 M      templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.csv
 M      templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii
 M      templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.csv
 M      templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii
 M      templates_MNI152NLin2009cAsym/T1.nii
 M      templates_MNI152NLin2009cAsym/TPM.nii
 M      templates_MNI152NLin2009cAsym/TPM_Age11.5.nii
 M      templates_MNI152NLin2009cAsym/Template_0_GS.nii
 M      templates_MNI152NLin2009cAsym/Template_1_Dartel.nii
 M      templates_MNI152NLin2009cAsym/Template_1_GS.nii
 M      templates_MNI152NLin2009cAsym/Template_2_Dartel.nii
 M      templates_MNI152NLin2009cAsym/Template_2_GS.nii
 M      templates_MNI152NLin2009cAsym/Template_3_Dartel.nii
 M      templates_MNI152NLin2009cAsym/Template_3_GS.nii
 M      templates_MNI152NLin2009cAsym/Template_4_Dartel.nii
 M      templates_MNI152NLin2009cAsym/Template_4_GS.nii
 M      templates_MNI152NLin2009cAsym/Template_5_Dartel.nii
 M      templates_MNI152NLin2009cAsym/Template_6_Dartel.nii
 M      templates_MNI152NLin2009cAsym/Template_T1.nii
 M      templates_MNI152NLin2009cAsym/aal3.csv
 M      templates_MNI152NLin2009cAsym/aal3.nii
MM      templates_MNI152NLin2009cAsym/aal3.txt
 M      templates_MNI152NLin2009cAsym/anatomy3.csv
 M      templates_MNI152NLin2009cAsym/anatomy3.nii
MM      templates_MNI152NLin2009cAsym/anatomy3.txt
 M      templates_MNI152NLin2009cAsym/brainmask.nii
 M      templates_MNI152NLin2009cAsym/cat.nii
 M      templates_MNI152NLin2009cAsym/cat_strokelesions_ATLAS303.nii
 M      templates_MNI152NLin2009cAsym/cat_wmh.nii
 M      templates_MNI152NLin2009cAsym/cat_wmh_miccai2017.nii
 M      templates_MNI152NLin2009cAsym/cobra.csv
 M      templates_MNI152NLin2009cAsym/cobra.nii
MM      templates_MNI152NLin2009cAsym/cobra.txt
 M      templates_MNI152NLin2009cAsym/hammers.csv
 M      templates_MNI152NLin2009cAsym/hammers.nii
MM      templates_MNI152NLin2009cAsym/hammers.txt
 M      templates_MNI152NLin2009cAsym/ibsr.csv
 M      templates_MNI152NLin2009cAsym/ibsr.nii
MM      templates_MNI152NLin2009cAsym/ibsr.txt
 M      templates_MNI152NLin2009cAsym/julichbrain.csv
 M      templates_MNI152NLin2009cAsym/julichbrain.nii
MM      templates_MNI152NLin2009cAsym/julichbrain.txt
 M      templates_MNI152NLin2009cAsym/lpba40.csv
 M      templates_MNI152NLin2009cAsym/lpba40.nii
MM      templates_MNI152NLin2009cAsym/lpba40.txt
 M      templates_MNI152NLin2009cAsym/mori.csv
 M      templates_MNI152NLin2009cAsym/mori.nii
MM      templates_MNI152NLin2009cAsym/mori.txt
 M      templates_MNI152NLin2009cAsym/neuromorphometrics.csv
 M      templates_MNI152NLin2009cAsym/neuromorphometrics.nii
MM      templates_MNI152NLin2009cAsym/neuromorphometrics.txt
MM      templates_MNI152NLin2009cAsym/schaefer.txt
MM      templates_MNI152NLin2009cAsym/templates.man
 M      templates_external/MNI152NLin2009cAsym.nii
 M      templates_external/MNI152NLin6Asym.nii
 M      templates_external/MNIColin27.nii
 M      templates_external/y_IXI555Dartel_to_MNI152NLin2009cAsym.nii
 M      templates_external/y_MNI152NLin6Asym_to_MNI152NLin2009cAsym.nii
 M      templates_external/y_MNIColin27_to_MNI152NLin2009cAsym.nii
A       templates_surfaces/lh.thickness.Template_T1
A       templates_surfaces/rh.thickness.Template_T1
A       templates_surfaces_32k/lh.thickness.Template_T1
A       templates_surfaces_32k/rh.thickness.Template_T1

Added: Added thickness values to new surface T1 templates.


------------------------------------------------------------------------
r1750 | gaser | 2021-01-11 23:43:04 +0100 (Mon, 11 Jan 2021) | 18 lines

Changed paths:
M       CHANGES.txt
MM      cat_vol_createMPM.m
M       html/cat_versions.html
A       templates_surfaces/lh.central.Template_T1.gii
D       templates_surfaces/mesh.central.Template_T1_IXI555_MNI152_GS.gii
D       templates_surfaces/mesh.inflated.freesurfer.gii
A       templates_surfaces/rh.central.Template_T1.gii
A       templates_surfaces_32k/lh.central.Template_T1.gii
D       templates_surfaces_32k/mesh.central.Template_T1_IXI555_MNI152_GS.gii
D       templates_surfaces_32k/mesh.inflated.freesurfer.gii
A       templates_surfaces_32k/rh.central.Template_T1.gii

(1) Changed: Updated new version information in html pages.
(2) Changed: Removed some surface mesh templates whoch are not needed anymore.
(3) Added:   Added new surface T1 templates.


------------------------------------------------------------------------
r1749 | gaser | 2021-01-11 22:15:04 +0100 (Mon, 11 Jan 2021) | 76 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_createMPM.m
M       cat_vol_defs.m
M       development/Anatomy2CAT12.m
A       development/JulichBrain2CAT12.m
A       development/Template_0_GS1mm.nii
A       development/Template_1_GS1mm.nii
A       development/Template_2_GS1mm.nii
A       development/Template_3_GS1mm.nii
A       development/Template_4_GS1mm.nii
D       development/Template_4_IXI555_MNI152_GS1mm_corr.nii
M       html/cat_versions.html
M       templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii
M       templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii
M       templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii
M       templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii
A       templates_MNI152NLin2009cAsym/T1.nii
A       templates_MNI152NLin2009cAsym/TPM.nii
M       templates_MNI152NLin2009cAsym/TPM_Age11.5.nii
A       templates_MNI152NLin2009cAsym/Template_0_GS.nii
D       templates_MNI152NLin2009cAsym/Template_0_IXI555_MNI152_GS.nii
A       templates_MNI152NLin2009cAsym/Template_1_Dartel.nii
A       templates_MNI152NLin2009cAsym/Template_1_GS.nii
D       templates_MNI152NLin2009cAsym/Template_1_IXI555_MNI152.nii
D       templates_MNI152NLin2009cAsym/Template_1_IXI555_MNI152_GS.nii
A       templates_MNI152NLin2009cAsym/Template_2_Dartel.nii
A       templates_MNI152NLin2009cAsym/Template_2_GS.nii
D       templates_MNI152NLin2009cAsym/Template_2_IXI555_MNI152.nii
D       templates_MNI152NLin2009cAsym/Template_2_IXI555_MNI152_GS.nii
A       templates_MNI152NLin2009cAsym/Template_3_Dartel.nii
A       templates_MNI152NLin2009cAsym/Template_3_GS.nii
D       templates_MNI152NLin2009cAsym/Template_3_IXI555_MNI152.nii
D       templates_MNI152NLin2009cAsym/Template_3_IXI555_MNI152_GS.nii
A       templates_MNI152NLin2009cAsym/Template_4_Dartel.nii
A       templates_MNI152NLin2009cAsym/Template_4_GS.nii
D       templates_MNI152NLin2009cAsym/Template_4_IXI555_MNI152.nii
D       templates_MNI152NLin2009cAsym/Template_4_IXI555_MNI152_GS.nii
A       templates_MNI152NLin2009cAsym/Template_5_Dartel.nii
D       templates_MNI152NLin2009cAsym/Template_5_IXI555_MNI152.nii
A       templates_MNI152NLin2009cAsym/Template_6_Dartel.nii
D       templates_MNI152NLin2009cAsym/Template_6_IXI555_MNI152.nii
A       templates_MNI152NLin2009cAsym/Template_T1.nii
D       templates_MNI152NLin2009cAsym/Template_T1_IXI555_MNI152_GS.nii
M       templates_MNI152NLin2009cAsym/aal3.nii
M       templates_MNI152NLin2009cAsym/anatomy3.nii
M       templates_MNI152NLin2009cAsym/anatomy3.txt
M       templates_MNI152NLin2009cAsym/brainmask.nii
M       templates_MNI152NLin2009cAsym/cat.nii
M       templates_MNI152NLin2009cAsym/cat_strokelesions_ATLAS303.nii
M       templates_MNI152NLin2009cAsym/cat_wmh.nii
M       templates_MNI152NLin2009cAsym/cat_wmh_miccai2017.nii
M       templates_MNI152NLin2009cAsym/hammers.nii
M       templates_MNI152NLin2009cAsym/ibsr.nii
M       templates_MNI152NLin2009cAsym/julichbrain.csv
M       templates_MNI152NLin2009cAsym/julichbrain.nii
M       templates_MNI152NLin2009cAsym/julichbrain.txt
M       templates_MNI152NLin2009cAsym/mori.nii
M       templates_MNI152NLin2009cAsym/neuromorphometrics.nii
A       templates_MNI152NLin2009cAsym/templates.man
A       templates_external/MNI152NLin2009cAsym.nii
A       templates_external/MNI152NLin6Asym.nii
A       templates_external/y_IXI555Dartel_to_MNI152NLin2009cAsym.nii
D       templates_external/y_MNI152NLin2009cAsym_to_IXI550Dartel.nii
D       templates_external/y_MNI152NLin6Asym_to_IXI550Dartel.nii
M       templates_external/y_MNI152NLin6Asym_to_MNI152NLin2009cAsym.nii
D       templates_external/y_MNIColin27_to_IXI550Dartel.nii
M       templates_external/y_MNIColin27_to_MNI152NLin2009cAsym.nii

(1) Changed: Updated Anatomy2CAT12 to tramsform Anatomy3 atlas to CAT12.
(2) Changed: Prepared new version information in html pages.
(3) Added:   Added JulichBrain2CAT12 to tramsform julichbrain atlas to CAT12.
(4) Fixed:   Corrected atlases in MNI152NLin2009cAsym (cobra/lpba40/ibsr in
             progress).
(5) Fixed:   cat_vol_defs can now correctly deal with 4D data.

------------------------------------------------------------------------
r1748 | gaser | 2021-01-08 17:19:26 +0100 (Fri, 08 Jan 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       html/cat.html
R       templates_volumes/anatomy3.csv
RM      templates_volumes/anatomy3.nii
R       templates_volumes/anatomy3.txt

Changed: Resolved issue with anatomy3-files.

------------------------------------------------------------------------
r1747 | gaser | 2021-01-08 16:58:17 +0100 (Fri, 08 Jan 2021) | 86 lines

Changed paths:
M       CHANGES.txt
D       aal.csv
        > moved to templates_volumes_not_distributed/aal.csv
D       aal.nii
        > moved to templates_volumes_not_distributed/aal.nii
D       aal.txt
        > moved to templates_volumes_not_distributed/aal.txt
M       cat_conf_ROI.m
M       cat_defaults.m
M       development/Anatomy2CAT12.m
A       templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.csv
M       templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii
A       templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.csv
M       templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii
A       templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.csv
M       templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii
A       templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.csv
M       templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii
M       templates_MNI152NLin2009cAsym/Template_T1_IXI555_MNI152_GS.nii
A       templates_MNI152NLin2009cAsym/aal3.csv
A       templates_MNI152NLin2009cAsym/aal3.txt
A       templates_MNI152NLin2009cAsym/anatomy3.csv
A       templates_MNI152NLin2009cAsym/anatomy3.nii
A       templates_MNI152NLin2009cAsym/anatomy3.txt
D       templates_MNI152NLin2009cAsym/catlog_main_20210106_163921_log01.txt
D       templates_MNI152NLin2009cAsym/catlog_main_20210106_163921_log02.txt
D       templates_MNI152NLin2009cAsym/catlog_main_20210106_163921_log03.txt
D       templates_MNI152NLin2009cAsym/catlog_main_20210106_163921_log04.txt
D       templates_MNI152NLin2009cAsym/catlog_main_20210106_163921_log05.txt
D       templates_MNI152NLin2009cAsym/catlog_main_20210106_163921_log06.txt
A       templates_MNI152NLin2009cAsym/cobra.csv
A       templates_MNI152NLin2009cAsym/cobra.nii
A       templates_MNI152NLin2009cAsym/cobra.txt
A       templates_MNI152NLin2009cAsym/hammers.csv
A       templates_MNI152NLin2009cAsym/hammers.nii
A       templates_MNI152NLin2009cAsym/hammers.txt
A       templates_MNI152NLin2009cAsym/ibsr.csv
A       templates_MNI152NLin2009cAsym/ibsr.nii
A       templates_MNI152NLin2009cAsym/ibsr.txt
A       templates_MNI152NLin2009cAsym/julichbrain.csv
M       templates_MNI152NLin2009cAsym/julichbrain.nii
A       templates_MNI152NLin2009cAsym/julichbrain.txt
A       templates_MNI152NLin2009cAsym/lpba40.csv
A       templates_MNI152NLin2009cAsym/lpba40.nii
A       templates_MNI152NLin2009cAsym/lpba40.txt
A       templates_MNI152NLin2009cAsym/mori.csv
A       templates_MNI152NLin2009cAsym/mori.nii
A       templates_MNI152NLin2009cAsym/mori.txt
A       templates_MNI152NLin2009cAsym/neuromorphometrics.csv
M       templates_MNI152NLin2009cAsym/neuromorphometrics.nii
A       templates_MNI152NLin2009cAsym/neuromorphometrics.txt
A       templates_MNI152NLin2009cAsym/schaefer.txt
A       templates_external/MNIColin27.nii
D       templates_external/old_template
D       templates_external/old_template/y_MNI152NLin6Asym_T1w.nii
        > moved to templates_external/y_MNI152NLin6Asym_to_IXI550Dartel.nii
D       templates_external/old_template/y_colin27_t1_tal_hires.nii
        > moved to templates_external/y_MNIColin27_to_IXI550Dartel.nii
D       templates_external/old_template/y_mni_icbm152_t1_tal_nlin_asym_09c.nii
        > moved to templates_external/y_MNI152NLin2009cAsym_to_IXI550Dartel.nii
A  +    templates_external/y_MNI152NLin2009cAsym_to_IXI550Dartel.nii
        > moved from templates_external/old_template/y_mni_icbm152_t1_tal_nlin_asym_09c.nii
A  +    templates_external/y_MNI152NLin6Asym_to_IXI550Dartel.nii
        > moved from templates_external/old_template/y_MNI152NLin6Asym_T1w.nii
A       templates_external/y_MNI152NLin6Asym_to_MNI152NLin2009cAsym.nii
A  +    templates_external/y_MNIColin27_to_IXI550Dartel.nii
        > moved from templates_external/old_template/y_colin27_t1_tal_hires.nii
A       templates_external/y_MNIColin27_to_MNI152NLin2009cAsym.nii
A       templates_volumes/anatomy3.csv
A       templates_volumes/anatomy3.nii
A       templates_volumes/anatomy3.txt
A  +    templates_volumes_not_distributed/aal.csv
        > moved from aal.csv
A  +    templates_volumes_not_distributed/aal.nii
        > moved from aal.nii
A  +    templates_volumes_not_distributed/aal.txt
        > moved from aal.txt

(1) Changed: Updated Anatomy2CAT12 to tramsform Anatomy3 atlas to CAT12.
(2) Changed: Updated description for atlas csv-files.
(3) Changed: Finished transforming all atlases to new MNI152NLin2009cAsym
             space. in templates_MNI152NLin2009cAsym.
(4) Changed: Added and updatd templates and deformation fields to other spaces
             in templates_external.

------------------------------------------------------------------------
r1746 | gaser | 2021-01-08 01:34:59 +0100 (Fri, 08 Jan 2021) | 87 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_conf_extopts.m
M       cat_conf_long.m
M       cat_defaults.m
M       cat_run_job.m
M       cat_run_job1639.m
A       cat_vol_createMPM.m
M       cat_vol_groupwise_ls.m
M       cat_vol_set_com.m
A       development/correct_tpm2one.m
D       development/y_MNI152NLin6Asym_T1w.nii
        > moved to templates_external/old_template/y_MNI152NLin6Asym_T1w.nii
D       development/y_colin27_t1_tal_hires.nii
        > moved to templates_external/old_template/y_colin27_t1_tal_hires.nii
D       development/y_mni_icbm152_t1_tal_nlin_asym_09c.nii
        > moved to templates_external/old_template/y_mni_icbm152_t1_tal_nlin_asym_09c.nii
 M      html/cat_methods_WMHC.html
 M      html/cat_methods_WMHC0.html
 M      html/cat_methods_WMHC1.html
 M      html/cat_methods_WMHC2.html
 M      html/cat_methods_WMHC3.html
 M      html/images/catreportj_OAS1_0031_MR1_mpr_n4_anon_sbj_111_WMHC0.jpg
 M      html/images/catreportj_OAS1_0031_MR1_mpr_n4_anon_sbj_111_WMHC1.jpg
 M      html/images/catreportj_OAS1_0031_MR1_mpr_n4_anon_sbj_111_WMHC2.jpg
 M      html/images/catreportj_OAS1_0031_MR1_mpr_n4_anon_sbj_111_WMHC3.jpg
D       internal/cat_vol_atlas.m
M       tbx_cfg_cat.m
A       templates_MNI152NLin2009cAsym
A       templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii
A       templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii
A       templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii
A       templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii
A       templates_MNI152NLin2009cAsym/TPM_Age11.5.nii
A       templates_MNI152NLin2009cAsym/Template_0_IXI555_MNI152_GS.nii
A       templates_MNI152NLin2009cAsym/Template_1_IXI555_MNI152.nii
A       templates_MNI152NLin2009cAsym/Template_1_IXI555_MNI152_GS.nii
A       templates_MNI152NLin2009cAsym/Template_2_IXI555_MNI152.nii
A       templates_MNI152NLin2009cAsym/Template_2_IXI555_MNI152_GS.nii
A       templates_MNI152NLin2009cAsym/Template_3_IXI555_MNI152.nii
A       templates_MNI152NLin2009cAsym/Template_3_IXI555_MNI152_GS.nii
A       templates_MNI152NLin2009cAsym/Template_4_IXI555_MNI152.nii
A       templates_MNI152NLin2009cAsym/Template_4_IXI555_MNI152_GS.nii
A       templates_MNI152NLin2009cAsym/Template_5_IXI555_MNI152.nii
A       templates_MNI152NLin2009cAsym/Template_6_IXI555_MNI152.nii
A       templates_MNI152NLin2009cAsym/Template_T1_IXI555_MNI152_GS.nii
A       templates_MNI152NLin2009cAsym/aal3.nii
A       templates_MNI152NLin2009cAsym/brainmask.nii
A       templates_MNI152NLin2009cAsym/cat.nii
A       templates_MNI152NLin2009cAsym/cat_strokelesions_ATLAS303.nii
A       templates_MNI152NLin2009cAsym/cat_wmh.nii
A       templates_MNI152NLin2009cAsym/cat_wmh_miccai2017.nii
A       templates_MNI152NLin2009cAsym/catlog_main_20210106_163921_log01.txt
A       templates_MNI152NLin2009cAsym/catlog_main_20210106_163921_log02.txt
A       templates_MNI152NLin2009cAsym/catlog_main_20210106_163921_log03.txt
A       templates_MNI152NLin2009cAsym/catlog_main_20210106_163921_log04.txt
A       templates_MNI152NLin2009cAsym/catlog_main_20210106_163921_log05.txt
A       templates_MNI152NLin2009cAsym/catlog_main_20210106_163921_log06.txt
A       templates_MNI152NLin2009cAsym/julichbrain.nii
A       templates_MNI152NLin2009cAsym/neuromorphometrics.nii
A       templates_external
A       templates_external/old_template
A  +    templates_external/old_template/y_MNI152NLin6Asym_T1w.nii
        > moved from development/y_MNI152NLin6Asym_T1w.nii
A  +    templates_external/old_template/y_colin27_t1_tal_hires.nii
        > moved from development/y_colin27_t1_tal_hires.nii
A  +    templates_external/old_template/y_mni_icbm152_t1_tal_nlin_asym_09c.nii
        > moved from development/y_mni_icbm152_t1_tal_nlin_asym_09c.nii
M       templates_volumes/neuromorphometrics.txt

(1) Changed: Updated atlas information.
(2) Changed: Started to remove old CAT12 versions from the GUI.
(3) Changed: Updated cat_vol_set_com.m to return affine tramsformation.
(4) Changed: Removed new_release field from cat_vol_groupwise_ls.m
(5) Changed: Added automatically setting of origin to cat_run_job* to get
             a reliable starting value for affine registration.
(6) Changed: Added extopts.setCOM field to cat_defaults and cat_conf_extopts.
(7) Deleted: Removed old cat_vol_atlas.m from folder "internal".
(8) Added:   Added tool to create maximum probabilty maps from labels and
             existing deformation fields.
(9) Added:   Created tool to correct last class in TPMs and GS-templates
             correct_tpm2one.m
(10) Added:  Started to switch to new MNI152NLin2009cAsym space and prepared
             templates_MNI152NLin2009cAsym and templates_external and added
             deformation fields to other spaces.

------------------------------------------------------------------------
r1745 | gaser | 2021-01-05 17:58:48 +0100 (Tue, 05 Jan 2021) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_main_roi.m
M       cat_stat_spm2x.m
M       cat_surf_render.m
M       cat_surf_results.m
M       cat_vol_slice_overlay.m
M       html/cat_methods_VBM.html
M       html/cat_methods_WMHC.html
M       html/cat_methods_WMHC2.html

(1) Changed: Updated help text.
(2) Changed: Updated atlas overlay output in cat_vol_slice_overlay.m
             and cat_stat_spm2x.m.
(3) Changed: Output warning if data were removed in cat_surf_results.m.
(4) Fixed:   Correction of data range in cat_surf_render.m.

------------------------------------------------------------------------
r1744 | dahnke | 2021-01-05 13:11:35 +0100 (Tue, 05 Jan 2021) | 29 lines

Changed paths:
M       CHANGES.txt
M       cat_io_report.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_reportstr.m
M       cat_vol_partvol.m
M       cat_vol_partvol1639.m
M       html/cat_FAQ.html
M       html/cat_methods.html
M       html/cat_methods_VBM.html
A       html/cat_methods_WMHC.html
A       html/cat_methods_WMHC0.html
A       html/cat_methods_WMHC1.html
A       html/cat_methods_WMHC2.html
A       html/cat_methods_WMHC3.html
A       html/images/catreportj_OAS1_0031_MR1_mpr_n4_anon_sbj_111_WMHC0.jpg
A       html/images/catreportj_OAS1_0031_MR1_mpr_n4_anon_sbj_111_WMHC1.jpg
A       html/images/catreportj_OAS1_0031_MR1_mpr_n4_anon_sbj_111_WMHC2.jpg
A       html/images/catreportj_OAS1_0031_MR1_mpr_n4_anon_sbj_111_WMHC3.jpg
!       templates_surfaces_32k/lh.central.freesurfer.gii
!       templates_surfaces_32k/lh.sphere.freesurfer.gii
!       templates_surfaces_32k/rh.central.freesurfer.gii
!       templates_surfaces_32k/rh.sphere.freesurfer.gii

(1)  Fixed:  Removed old WMH variables in cat_main and update WMHC help.
(2)  Fixed:  Corrected histogram error in cat_io_report.


------------------------------------------------------------------------
r1743 | dahnke | 2021-01-03 12:15:14 +0100 (Sun, 03 Jan 2021) | 38 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_main_clean_gwc.m
M       cat_main_reportfig.m
M       cat_run.m
M       cat_spm_results_ui.m
M       cat_stat_spm2x.m
M       cat_surf_info.m
M       cat_surf_render2.m
M       cat_surf_resamp.m
M       cat_surf_results.m
M       cat_surf_scaling.m
 M      development/Anatomy2CAT12.m
M       tbx_cfg_cat.m
 M      templates_volumes_not_distributed/aparc_DKT40.nii
 M      templates_volumes_not_distributed/aparc_a2009s.nii

(1)  Changed: Updated the structure of cat_surf_parameters (& cat_conf_stools),
              corrected some bugs and added comments.
(2)  Fixed:   Corrected tiny bugs in cat_main_reportfig and tbx_cfg_cat.
(3)  Fixed:   Corrected bugs in batch processing in cat_spm_results_ui and
              added spm_run_results as internal function.
(4)  Fixed:   Added missing variable in cat_stat_spm2x.
(5)  Fixed:   Corrected XML setting in cat_surf_info.
(6)  Fixed:   Corrected tiny bug in cat_surf_render2.
(7)  Fixed:   Corrected little bug in file list merging in cat_surf_resamp.
              Corrected bug when the subject name include similar string that
              should be replaced in the texture field. Try to catch more special
              cases and added counter for different cases.
(8)  Fixed:   Corrected batch handling of cat_surf_results for missing input, eg.
              if cat_stat_spm2x create no output due to insignificant result.
(9)  Fixed:   Tiny changes in cat_surf_scaling.
(10) Fixed:   Corrected lazy settings in cat_run.
(11) Fixed:   Corrected skull-stripping problems in cat_main_clean_gwc.



------------------------------------------------------------------------
r1742 | gaser | 2020-12-30 13:54:50 +0100 (Wed, 30 Dec 2020) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_main1639.m
M       cat_main_roi.m
M       cat_stat_spm2x.m
M       cat_vol_defs.m

(1) Changed: Prepared cat_vol_defs.m for external call and output variable.
(2) Fixed:   Solved issues in cat_stat_spm2x.m if no extent threshold was
             exceeded.
(3) Fixed:   Removed some typos.

------------------------------------------------------------------------
r1741 | gaser | 2020-12-11 14:51:55 +0100 (Fri, 11 Dec 2020) | 55 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Kmeans.c
M       KmeansMex.c
M       Makefile
M       cat12.sh
M       cat_batch_cat.sh
M       cat_batch_long.sh
M       cat_batch_spm.sh
M       cat_conf_opts.m
M       cat_main_gintnorm.m
M       cat_main_gintnorm1639.m
M       cat_main_kamap.m
M       cat_run1173/cat_run_job1173.m
M       cat_run1173plus/cat_run_job1173plus.m
M       cat_run1445/cat_run_job1445.m
M       cat_run1445/cat_run_job_APP_init10701445.m
M       cat_run1585/cat_main_kamap1585.m
M       cat_run1585/cat_run_job1585.m
M       cat_run1585/cat_run_job_APP_init10701585.m
M       cat_run1585/cat_run_job_APP_init1585.m
M       cat_run1585/cat_run_job_APRGs1585.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_run_job_APP_init.m
M       cat_run_job_APP_init1070.m
M       cat_run_job_APRGs.m
M       cat_stat_check_cov2.m
A  +    cat_stat_kmeans.m
        > moved from kmeans3D.m
M       cat_surf_fun.m
M       cat_tst_qa_cleaner.m
M       cat_vol_iscale.m
M       check_pipeline.sh
M       distribute_to_server.sh
M       html/cat.html
D       kmeans3D.m
        > moved to cat_stat_kmeans.m
M       standalone/cat_parallelize.sh
M       standalone/cat_standalone.sh
M       standalone/cat_standalone_segment.txt
M       standalone/cat_standalone_segment_long.txt
A       templates_volumes_not_distributed/aparc_DKT40.nii
A       templates_volumes_not_distributed/aparc_a2009s.nii

(1) Changed: Updated atlas information in batch scripts.
(2) Changed: Added all options from cat12.sh to cat_batch_cat.sh.
(3) Changed: Replace cat12.sh by cat_batch_cat.sh and add deprecation warning
             to cat12.sh which should used anymore.
(4) Changed: Renamed kmeans3D.m to cat_vol_kmeans.m and changed all calls in
             functions.
(5) Changed: Updated cat_vol_kmeans.m to increase computation speed.


------------------------------------------------------------------------
r1740 | dahnke | 2020-12-01 12:47:53 +0100 (Tue, 01 Dec 2020) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_main_reportstr.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_spm_preproc8.m
M       cat_vol_qa.m

(1) Fixed:   Corrected further bug in cat_main_reportstr.
(2) Fixed:   Corrected handling of in-optimal SPM preprocessing in cat_run_job(1639)
             and increased minimum number of iterations in cat_spm_preproc8.
(3) New:     Added log-likelihood parameter to XML output in cat_vol_qa.

------------------------------------------------------------------------
r1739 | gaser | 2020-11-27 11:26:34 +0100 (Fri, 27 Nov 2020) | 40 lines

Changed paths:
D       Anatomy2Dartel.txt
M       CHANGES.txt
M       cat_conf_ROI.m
M       cat_conf_long.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_long_main.m
M       cat_surf_fun.m
D       cat_vol_atlas.m
        > moved to development/cat_vol_atlas.m
A       development/Anatomy2CAT12.m
A  +    development/cat_vol_atlas.m
        > moved from cat_vol_atlas.m
M       html/cat_instruction_templates.html
M       html/cat_licences.html
M       html/cat_methods_QA.html
M       html/cat_methods_RBM.html
D       templates_volumes/anatomy.csv
        > moved to templates_volumes_not_distributed/anatomy.csv
D       templates_volumes/anatomy.nii
        > moved to templates_volumes_not_distributed/anatomy.nii
D       templates_volumes/anatomy.txt
        > moved to templates_volumes_not_distributed/anatomy.txt
M       templates_volumes/julichbrain.txt
A       templates_volumes_not_distributed
A  +    templates_volumes_not_distributed/anatomy.csv
        > moved from templates_volumes/anatomy.csv
A  +    templates_volumes_not_distributed/anatomy.nii
        > moved from templates_volumes/anatomy.nii
A  +    templates_volumes_not_distributed/anatomy.txt
        > moved from templates_volumes/anatomy.txt

(1) Changed: Replaced old Anatomy atlas with newest version 3.
(2) Changed: Updated atlas information.
(3) Changed: Replaced old Anatomy2Dartel.txt by Anatomy2CAT12.m.
(4) Changed: Reformatted cat_long_main.m.
(5) Chnaged: Set default filetpye for head trimming to "same".
(6) Changed: Moved old anatomy atlas to templates_volumes_not_distributed.

------------------------------------------------------------------------
r1738 | gaser | 2020-11-25 17:14:31 +0100 (Wed, 25 Nov 2020) | 8 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cat_spm_results_ui.m

(1) Changed: Updated cat_spm_results_ui.m to work with both, CAT12 and TFCE.
(2) Changed: Makefile now copies cat_spm_results_ui.m to tfce folder if updated.

------------------------------------------------------------------------
r1737 | gaser | 2020-11-25 11:50:09 +0100 (Wed, 25 Nov 2020) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_cat.m
M       cat_plot_boxplot.m
 M      development/y_MNI152NLin6Asym_T1w.nii

Fixed: cat12.sh and cat_batch_cat.m had issues with multiples files if length of
       filenames differed.

------------------------------------------------------------------------
r1736 | dahnke | 2020-11-24 13:48:41 +0100 (Tue, 24 Nov 2020) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_run.m
M       cat_surf_info.m
M       cat_surf_parameters.m
M       cat_surf_resamp.m

(1) Fixed:   Removed temporar setting in lazy preprocessing in cat_run.
(2) Fixed:   Corrected settings for cerebellar processing in
             cat_surf_parameters and cat_surf_resamp.
(3) Fixed:   Corrected XML setting in cat_surf_info.


------------------------------------------------------------------------
r1735 | gaser | 2020-11-23 10:33:31 +0100 (Mon, 23 Nov 2020) | 12 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       Makefile
A       development/y_MNI152NLin6Asym_T1w.nii
M       html/cat.html

(1) Added:   Added deformation field for atlases based on MNI152NLin6Asym_T1w.
(2) Changed: Precompiled packages are now also versioned to better support
             docker and singularity containers.

------------------------------------------------------------------------
r1734 | gaser | 2020-11-19 13:07:31 +0100 (Thu, 19 Nov 2020) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_conf_long.m
M       cat_surf_surf2roi.m
M       html/cat.html

(1) Changed: Experimental long. bias correction was moved to developer mode.
(2) Fixed:   Extraction ROI-based surface values for Schaefer atlases resulted
             in NaNs because label definition was not corrected (thanks to
             Thomas Zeffiro amd Felix Hoffstaedter for pointing to that issue).

------------------------------------------------------------------------
r1733 | gaser | 2020-11-16 15:16:43 +0100 (Mon, 16 Nov 2020) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
MM      cat_long_biascorr.m
M       html/cat.html

Fixed: cat_surf_map_atlas should now run also under Windows. CAT_ResampleSurf
       had difficulties in reading txt-files.

------------------------------------------------------------------------
r1732 | dahnke | 2020-11-13 21:41:29 +0100 (Fri, 13 Nov 2020) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_io_csv.m
M       cat_long_biascorr.m
M       cat_main_roi.m
M       cat_spm_results_ui.m
M       cat_surf_calc.m
MM      cat_vol_testflipping.m

(1) Fixed:   Corrected bug in cat_spm_results_ui.
(2) Fixed:   Corrected bug in cat_main_roi.

------------------------------------------------------------------------
r1731 | gaser | 2020-11-13 17:36:03 +0100 (Fri, 13 Nov 2020) | 29 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat12.sh
M       cat_batch_cat.m
M       cat_batch_cat.sh
M       cat_conf_long.m
M       cat_long_main.m
M       cat_main_kamap.m
M       cat_run_job.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_display.m
M       cat_surf_map_atlas.m
M       cat_vol_testflipping.m
M       html/cat.html

(1) Changed: Switch to developer mode for cat_surf_display for anootation files.
(2) Changed: Added hidden option for disabling use of longitudinal TPM in long.
             pipeline.
(3) Fixed:   Corrected bug for resampling fsaverage to individual surfaces which
             was not working for Windows systems. Now we temporarily save the
             annotation label as txt file and resample it and convert it to
             annotation file back.
(4) Fixed:   cat_amap1639 was not existing for use in cat_main_kamap.m
(5) Fixed:   Corrected handling of folders or filenames with spaces in shell
             scripts and cat_batch_cat.m

------------------------------------------------------------------------
r1730 | dahnke | 2020-11-11 15:18:47 +0100 (Wed, 11 Nov 2020) | 21 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_long.m
M       cat_conf_tools.m
M       cat_io_cmd.m
A       cat_long_biascorr.m
M       cat_long_createTPM.m
M       cat_long_main.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m
M       cat_main_updateSPM1639.m
M       cat_run.m
M       cat_run_job.m

(1) Fixed:    Corrected issue in case of bad SPM backgrounds.
(2) Fixed:    Corrected bug in setting SPM bias correction in longitudinal case.
(3) Fixed:    Corrected bug with NaNs and minimum probability in cat_long_createTPM.
(4) Fixed:    Corrected number of digits in relative volume in case of WMHs.
(5) New:      Beta version of a longitudinal bias correction.


------------------------------------------------------------------------
r1729 | dahnke | 2020-11-07 11:39:47 +0100 (Sat, 07 Nov 2020) | 30 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_io_addwarning.m
M       cat_io_colormaps.m
M       cat_io_report.m
M       cat_long_main.m
M       cat_main.m
M       cat_main1639.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_simple.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_parameters.m
M       cat_surf_resamp.m
A       cat_vol_testflipping.m
M       tbx_cfg_cat.m

(1) New:       Added warning in case of possibly flipped images in cat_run_job.
							 Added flipping test cat_vol_testflipping but it did not work yet.
(2) Fixed:     Corrected bugs in error report in cat_io_report.
(3) Fixed:     Corrected dependencies in cat_simple.
(4) Changed:   Removed files in surface preview pipeline.
(5) Fixed.     Corrected tissue values in cat_report in case of WMHs & WMHC<2.


------------------------------------------------------------------------
r1728 | gaser | 2020-10-27 14:10:21 +0100 (Tue, 27 Oct 2020) | 22 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_run_job1639.m
M       cat_sanlm.m
M       cat_surf_map_atlas.m
M       cat_surf_results.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_ui.m
M       html/cat.html
MM      standalone/cat_standalone_tfce.txt

(1) Changed: Extended cat_vol_slice_overlay.m by new option to control slice
             overview and removed some smaller inconsistencies.
(2) Changed: Updated cat_vol_slice_overlay_ui.m to consider new options.
(3) Changed: Added experimental support for cat_surf_results to display slice
             overlay for volume data.
(4) Fixed:   Added missing input parameter to cat_sanlm.m.
(5) Fixed:   Calling cat_surf_map_atlas.m with input arguments was crashing.
             Furthermore, mapped annot files are now saved in label instead
             than surf folder (Thanks to Francois Tadel for pointing to this).

------------------------------------------------------------------------
r1727 | gaser | 2020-10-23 14:25:02 +0200 (Fri, 23 Oct 2020) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_long_main.m
M       cat_stat_spm.m

Fixed: Resolved issues with longitudinal model for large changes over time from
       release r1725 and resulted in distorted segmentations.

------------------------------------------------------------------------
r1726 | gaser | 2020-10-21 15:11:56 +0200 (Wed, 21 Oct 2020) | 70 lines

Changed paths:
 M      Amap.c
 M      Bayes.c
 M      BayesMex.c
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
 M      Kmeans.c
 M      KmeansMex.c
M       Makefile
 M      MrfPrior.c
 M      Pve.c
 M      WarpPriors.c
 M      cat_amap.c
M       cat_conf_ROI.m
M       cat_conf_long.m
M       cat_long_main.m
M       cat_long_multi_run.m
M       cat_plot_boxplot.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_stat_analyze_ROIs.m
D       cat_stat_results.m
        > moved to development/cat_stat_results.m
M       cat_stat_spm.m
M       cat_surf_results.m
 M      cat_vbdist.c
 M      cat_vol_ROIval.c
 M      cat_vol_downcut.c
 M      cat_vol_eidist.c
 M      cat_vol_eikonal3.c
 M      cat_vol_genus0.c
 M      cat_vol_gradient3.c
 M      cat_vol_laplace3.c
 M      cat_vol_localstat.c
 M      cat_vol_median3.c
 M      cat_vol_median3c.c
M       cat_vol_pbt.m
M       cat_vol_pbt2.m
 M      cat_vol_pbtp.c
 M      cat_vol_pbtp2.c
M       cat_vol_set_com.m
A  +    development/cat_stat_results.m
        > moved from cat_stat_results.m
 M      genus0.c
M       html/cat.html
M       html/cat.txt
M       html/cat_methods_LP.html
 M      optimizer3d.c
 M      sanlm_float.c
M       standalone/cat_standalone.sh
A       standalone/cat_standalone_tfce.txt
M       templates_volumes/cobra.txt

(1) Changed: Added TFCE batch to standalone scripts.
(2) Moved:   Moved cat_stat_results.m to development folder.
(3) Changed: Do not accept analysis of diff-files in cat_stat_analyze_ROIs.m
(4) Changed: Do not call for inverse effects for F-test
             in cat_stat_analyze_ROIs.m
(5) Changed: Print warning if output voxel size is changed and use defaul voxel
             size for longitudinal pipeline.
(6) Changed: Prepared longitudinal pipeline to save both longitudinal models.
(7) Changed: Added cleaning of folder and correction of file permissions to
             Makefile (thanks to Dimitri Papadopoulos for pointing to that
             issue).
(8) Fixed:   Corrected many typos in help text.
(9) Fixed:   Saving of empty dataplot png-file in cat_surf_results.m is now
             prevented.


------------------------------------------------------------------------
r1725 | gaser | 2020-10-14 09:53:20 +0200 (Wed, 14 Oct 2020) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_run_newcatch.m
M       cat_vol_groupwise_ls.m
M       check_pipeline.sh
M       check_pipeline_homogeneity.m
M       html/cat.html

(1) Changed: Added warning if new experimental pipeline is used to
             cat_run_newcatch.m
(2) Changed: Changed selection filter for only recognizing newer longitudinal
             data in check_pipeline_homogeneity.m
(3) Fixed:   Corrected recognition of "large" flag in check_pipeline.sh.


------------------------------------------------------------------------
r1724 | gaser | 2020-10-13 15:34:13 +0200 (Tue, 13 Oct 2020) | 26 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_io_report.m
M       cat_io_rerun.m
M       cat_main_reportfig.m
M       cat_parallelize.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_surf_create_TPM_hull_surface.m
M       cat_vol_groupwise_ls.m
M       html/cat.html

(1) Changed: Again changed handling of negative and background values in
             cat_vol_groupwise_ls.m.
(2) Changed: Print warning if head TPM surface could not be saved in
             templates_surfaces.
(3) Changed: Check whether scaling of affine transformation is getting too small
             between different levels of affine registration. This should
             prevent that TPM is poorly fitted to data and makes affine
             registration more stable.
(4) Fixed:   Corrected typo in cat_parallelize.m.
(5) Fixed:   Data with large offset (scl_inter) were not correctly globally
             scaled in cat_vol_groupwise_ls.m


------------------------------------------------------------------------
r1723 | gaser | 2020-10-08 10:17:19 +0200 (Thu, 08 Oct 2020) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_results.m
M       cat_vol_groupwise_ls.m

(1) Changed: Negative values in cat_vol_groupwise_ls.m are now corrected more
             appropriatly to prevent issues with subsequent processing
             functions.
(2) Changed: Additionally save dataplot in cat_surf_results.m.
(3) Fixed:   Corrected size of saved ROI meshes w.r.t. to original mesh size
             (32k vs 164k) in cat_stat_analyze_ROIs.m.
(4) Fixed:   Corrected data cursor selection for volume data in
             cat_surf_results.m.


------------------------------------------------------------------------
r1722 | gaser | 2020-10-02 12:11:40 +0200 (Fri, 02 Oct 2020) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat12.sh
M       cat_batch_cat.sh
M       cat_batch_long.sh
M       cat_main1639.m
M       cat_stat_analyze_ROIs.m
M       cat_vol_groupwise_ls.m

(1) Changed: Negative values in cat_vol_groupwise_ls.m are now corrected more
             appropriatly to prevent issues with subsequent processing
             functions.
(2) Changed: optimized output of p-values in cat_stat_analyze_ROIs.m.
(3) Fixed:   Corrected some inconsistencies in shell scripts with relative
             and absolute paths.
(4) Changed: TFCE estimation is now directly called vioa CAT12 GUI.

------------------------------------------------------------------------
r1721 | gaser | 2020-09-25 22:30:41 +0200 (Fri, 25 Sep 2020) | 28 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.sh
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_parallelize.m
M       cat_run_job.m
M       cat_run_job_APP_SPMinit.m
M       cat_spm_affreg.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_info.m
M       cat_surf_parameters.m
M       cat_update.m
M       cat_vol_approx.m
M       cat_vol_qa.m
M       html/cat.html

(1) Changed: Added seed for random number generator to many files to ensure
             consistency and reliability of segmentations.
(2) Changed: Supress warning in cat_update.m.
(3) Fixed:   Changed handling of texture and dataname field in cat_surf_info
             that failed for some files.
(4) Changed: Added check for fopen status in cat_parallelize that prevents
             error messages if a new batch is opened before the parallel batch
             is finished.
(5) Changed: Check for full path if necessary in at12.sh

------------------------------------------------------------------------
r1720 | gaser | 2020-09-21 11:06:51 +0200 (Mon, 21 Sep 2020) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       html/cat.html

Changed: Renamed RC2 to final CAT12.7.

------------------------------------------------------------------------
r1719 | gaser | 2020-09-16 17:45:20 +0200 (Wed, 16 Sep 2020) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_main1639.m
M       cat_main_reportfig.m
M       cat_surf_createCS.m
M       cat_surf_fun.m

(1) Changed: Preveiw surfaces and surf/fast folder are now deleted after report.
(2) Changed: Commented out call to saveico in cat_surf_createCS for fast track.

------------------------------------------------------------------------
r1718 | gaser | 2020-09-16 15:59:35 +0200 (Wed, 16 Sep 2020) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_long_createTPM.m
M       cat_stat_spm2x.m
M       html/cat_statistics.html

(1) Changed: Added conversion to z-image to cat_stat_spm2x.m
(2) Fixed:   Changed criteria to compare voxel sizes in cat_long_createTPM.m to
             prevent rounding issues.

------------------------------------------------------------------------
r1717 | gaser | 2020-09-14 13:06:18 +0200 (Mon, 14 Sep 2020) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_spm_results_ui.m
MM      development/cat_vol_multiply.m
 M      development/y_colin27_t1_tal_hires.nii
 M      development/y_mni_icbm152_t1_tal_nlin_asym_09c.nii
M       html/cat.html
 M      templates_volumes/julichbrain.csv
 M      templates_volumes/julichbrain.nii
MM      templates_volumes/julichbrain.txt

Fixed:  Corrected call to tfce_list and spm_list in cat_spm_results_ui.m.

------------------------------------------------------------------------
r1716 | gaser | 2020-09-11 22:22:01 +0200 (Fri, 11 Sep 2020) | 19 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_io_writenii.m
M       cat_long_main.m
M       cat_stat_analyze_ROIs.m
M       cat_stat_check_SPM.m
M       html/cat.html
M       html/cat_methods_RBM.html

(1) Fixed:  Corrected link to julichbrain-files in htlm documentation.
(2) Fixed:  Corrected call of rectangle command (thanks to James Ford for
            pointing to that issue) in cat_stat_check_SPM.m.
(3) Fixed:  Corrected handling of ROI results that only has inverse effects in
            cat_stat_analyze_ROIs.m
(4) Fixed:  Removed output argument for calling of spm_smooth in
            cat_io_writenii.m.


------------------------------------------------------------------------
r1715 | gaser | 2020-09-08 17:51:01 +0200 (Tue, 08 Sep 2020) | 43 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_defaults.m
M       cat_io_report.m
M       cat_long_shoot_defaults.m
M       cat_main_reportfig.m
M       cat_main_write.m
M       cat_run.m
M       cat_vol_ctype.m
M       cat_vol_defs.m
A       development/cat_vol_multiply.m
A       development/y_colin27_t1_tal_hires.nii
A       development/y_mni_icbm152_t1_tal_nlin_asym_09c.nii
M       html/cat.html
M       html/cat_licences.html
M       html/cat_methods_RBM.html
D       html/images/CAT_surf_atlas_neuromorphometics.png
        > moved to html/images/CAT_surf_atlas_neuromorphometrics.png
A  +    html/images/CAT_surf_atlas_neuromorphometrics.png
        > moved from html/images/CAT_surf_atlas_neuromorphometics.png
M       standalone/cat_standalone.sh
M       standalone/cat_standalone_segment.txt
M       standalone/cat_standalone_segment_long.txt
M       standalone/cat_standalone_simple.txt
M       templates_volumes/anatomy.txt
A       templates_volumes/julichbrain.csv
A       templates_volumes/julichbrain.nii
A       templates_volumes/julichbrain.txt

(1) Changed: Replaced flip-command by flipud to ensure compatibility to older
             Matlab version < R2013
(2) Fixed:   Added msiing identity function to cat_vol_defs.m.
(3) Added:   Added new JulichBrain Atlas v2.0 (thanks to Felix Hoffstaedter to
             provide a modified version of that atlas).
(4) Changed: Updated atlas information in online help and cat_defaults.m
(5) Changed: Set Cobra atlas as default in cat_defaults.m.
(6) Fixed:   Maximum value is checked for writing native atlases to prevent
             cutting of high values for uint16 data.
(7) Changed: Added webloc file for downloading MCR v93 files and updated
             help functions in cat_standalone.sh.

------------------------------------------------------------------------
r1714 | gaser | 2020-09-07 15:55:54 +0200 (Mon, 07 Sep 2020) | 26 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_amap.mexa64
M       cat_ornlm.mexa64
M       cat_sanlm.mexa64
M       cat_vbdist.mexa64
M       cat_vol_downcut.mexa64
M       cat_vol_eidist.mexa64
M       cat_vol_genus0.mexa64
M       cat_vol_gradient3.mexa64
M       cat_vol_interp3f.mexa64
M       cat_vol_laplace3.mexa64
M       cat_vol_laplace3R.mexa64
M       cat_vol_localstat.mexa64
M       cat_vol_median3.mexa64
M       cat_vol_median3c.mexa64
M       cat_vol_pbtp.c
M       cat_vol_pbtp.mexa64
M       cat_vol_pbtp2.c
M       cat_vol_simgrow.mexa64
M       html/cat.html

Changed: Recompiled mex-files for Linux with older Ubuntu 14.10.

------------------------------------------------------------------------
r1713 | gaser | 2020-09-07 14:56:16 +0200 (Mon, 07 Sep 2020) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat12.m
M       cat_spm_results_ui.m
M       cat_stat_check_SPM.m
M       html/cat.html

(1) Fixed:   Changed Units from Point to Pixel in some functions to get rid
             of display issues with Linux.
(2) Changed: Updated Makefile.

------------------------------------------------------------------------
r1712 | gaser | 2020-09-04 19:45:05 +0200 (Fri, 04 Sep 2020) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main_reportstr.m
M       cat_plot_boxplot.m
M       html/cat.html

Fixed: Replaced strange pragma, that caused issues in cat_main_reportstr.m
       and to be on the safe side also in cat_plot_boxplot.m.

------------------------------------------------------------------------
r1711 | gaser | 2020-09-03 17:46:07 +0200 (Thu, 03 Sep 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       compile.m

Changed: Added compile.m to the distribution.

------------------------------------------------------------------------
r1710 | gaser | 2020-09-03 10:59:16 +0200 (Thu, 03 Sep 2020) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_run.m

Fixed:   Windows user names with spaces cause trouble with parallel processing
         in cat_run.m. Thanks to Brendan Balken for providing a solution for
         that.

------------------------------------------------------------------------
r1709 | gaser | 2020-09-02 12:53:33 +0200 (Wed, 02 Sep 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_main_reportfig.m
M       cat_run_job1639.m

Fixed:   Try to catch some errors in cat_run_job1639.m and cat_main_reportfig.m

------------------------------------------------------------------------
r1708 | gaser | 2020-09-01 22:32:02 +0200 (Tue, 01 Sep 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_render.m

Fixed:   Structure sinfo1 has not only one entry in cat_surf_render.m
         (Thanks to Ningkai Wang for pointing to that error).

------------------------------------------------------------------------
r1707 | gaser | 2020-09-01 21:56:29 +0200 (Tue, 01 Sep 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_io_writenii.m
M       cat_main_roi.m

Fixed:   Catched call to spm_diffeo('pull') for older SPM12 versions.

------------------------------------------------------------------------
r1706 | gaser | 2020-09-01 21:48:12 +0200 (Tue, 01 Sep 2020) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_io_writenii.m

Fixed:   Catched call to spm_diffeo('pull') for older SPM12 versions.

------------------------------------------------------------------------
r1705 | gaser | 2020-08-31 22:49:54 +0200 (Mon, 31 Aug 2020) | 36 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_amap.mexa64
M       cat_conf_stools.m
M       cat_conf_tools.m
MM      cat_long_main.m
M       cat_ornlm.mexa64
M       cat_sanlm.mexa64
M       cat_stat_TIV.m
M       cat_update.m
M       cat_vbdist.mexa64
M       cat_vol_downcut.mexa64
M       cat_vol_eidist.mexa64
M       cat_vol_genus0.mexa64
M       cat_vol_gradient3.mexa64
M       cat_vol_interp3f.mexa64
M       cat_vol_laplace3.mexa64
M       cat_vol_laplace3R.mexa64
M       cat_vol_localstat.mexa64
M       cat_vol_median3.mexa64
M       cat_vol_median3c.mexa64
M       cat_vol_pbtp.mexa64
M       cat_vol_simgrow.mexa64
M       html/cat.html
M       html/cat.txt
M       html/cat_starting.html
M       html/cat_versions.html

(1) Fixed:   Recompiled Linux mex-files with Ubuntu 17.10.
(2) Changed: Updated help text.
(3) Changed: Print version information after update if release number was older.
(4) Changed: Updated filter for xml-file selection.

------------------------------------------------------------------------
r1704 | gaser | 2020-08-26 18:21:43 +0200 (Wed, 26 Aug 2020) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
D       cat_long_main.txt
M       check_pipeline.sh
M       html/cat.html

(1) Fixed:   Corrected copying of long. batch files.
(2) Fixed:   Corrected shell script for longitudinal batch.
(3) Removed: Removed cat_long_main.txt, which is now copied from
             cat_long_main.m



------------------------------------------------------------------------
r1703 | gaser | 2020-08-26 17:59:33 +0200 (Wed, 26 Aug 2020) | 28 lines

Changed paths:
M       CHANGES.txt
M       Makefile
A       cat_long_main.m
M       cat_long_main.txt
D       cat_long_mainShoot.txt
M       cat_long_multi_run.m
M       cat_main_registration.m
M       cat_main_registration2.m
M       cat_run.m
M       cat_stat_check_cov.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       tbx_cfg_cat.m

(1) Changed: Updated longitudinal pipeline and now only use cat_long_main.m
             for both longitudinal models.
(2) Changed: Updated and corrected dependencies in longitudinal batch.
(3) Changed: Updated dependencies in CAT12 segmentation for some files.
(4) Changed: Updated help texts.
(5) Changed: Set boxplot as default in cat_stat_check_cov.m.
(6) Changed: Updated Makefile.
(7) Changed: Temporarily removed cat_simple from GUI because iT is not working yet.
(8) Fixed:   Corrected use of positive Jacobian determinant in
             cat_main_registration*.m.



------------------------------------------------------------------------
r1702 | gaser | 2020-08-25 14:15:47 +0200 (Tue, 25 Aug 2020) | 17 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_conf_output.m
M       cat_io_volctype.m
M       cat_main_gintnorm.m
M       cat_main_gintnorm1639.m
M       cat_surf_render2.m
M       cat_surf_results.m
M       cat_vol_pbt.m
M       cat_vol_pbt2.m
M       cat_vol_sanlm.m
M       html/cat.html

Changed: Updated help texts and comments.

------------------------------------------------------------------------
r1701 | dahnke | 2020-08-24 14:05:58 +0200 (Mon, 24 Aug 2020) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_output.m
M       cat_main1639.m
M       cat_main_gintnorm.m
M       cat_main_reportcmd.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_run.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_render2.m
M       tbx_cfg_cat.m

(1) Fixed:     Corrected bug for missing res.ppe Variable in cat_main_gintnorm.
(2) Changed:   Added preview surfaces setting in cross-sectional pipeline.
(3) Fixed:     Define fonts in cat_main_reportfig.

------------------------------------------------------------------------
r1700 | gaser | 2020-08-24 13:34:06 +0200 (Mon, 24 Aug 2020) | 17 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       Makefile
M       check_pipeline/batch_surface_pipeline.m
M       html/cat.html
M       html/cat_versions.html
M       standalone/cat_standalone.sh
M       standalone/cat_standalone_segment.txt
M       standalone/cat_standalone_segment_long.txt

(1) Changed: Added standalone folder to precompiled CAT12 versions.
(2) Changed: Updated help text for cat_standalone.sh.
(3) Fixed:   Corrected directory dependencies in standalone batch files.


------------------------------------------------------------------------
r1699 | gaser | 2020-08-24 09:58:11 +0200 (Mon, 24 Aug 2020) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_analyze_ROIs.m
M       cat_vol_slice_overlay_ui.m
M       html/cat.html
M       spm_cat12.m
MM      templates_volumes/schaefer.txt

(1) Changed: Added check for Gatekeeper on MAC OS if binaries could not be
             executed in spm_cat12.m
(2) Fixed:   Corrected atlas name in cat_vol_slice_overlay_ui.m.
(4) Fixed:   Added missing path to batch mode in cat_stat_analyze_ROIs.m.


------------------------------------------------------------------------
r1698 | gaser | 2020-08-24 09:22:21 +0200 (Mon, 24 Aug 2020) | 22 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_main.m
 M      cat_main_clean_gwc1639.m
M       cat_main_kamap.m
M       cat_run_job1639.m
M       html/cat.html
M       html/cat_licences.html
M       html/cat_methods_RBM.html
M       html/cat_versions.html
M       tbx_cfg_cat.m

(1) Changed: Many updates to atlas information in online help.
(2) Changed: Also use cat_main_amap1639 instead of cat_main_amap  in cat_main.m
             and cat_main_kamap.m
(3) Changed: Suppress warning for creating already existing directories in
             cat_run_job1639.m.
(4) Fixed:   Added missing inv_weighting field to cat_main.m.


------------------------------------------------------------------------
r1697 | gaser | 2020-08-20 16:08:04 +0200 (Thu, 20 Aug 2020) | 26 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_install_atlases.m
M       cat_long_multi_run.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_run_newcatch.m
M       cat_surf_calc.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_vol_atlas.m
M       cat_vol_createTPM.m
M       html/cat.html
M       html/cat_licences.html
M       html/cat_methods_RBM.html
M       templates_volumes/mori.txt
A       templates_volumes/schaefer.txt

(1) Changed: Many updates to atlas information in online help.
(2) Changed: Added 'f' flag to copyfile calls because of rare file permission
             issues.
(3) Changed: Updated Makefile.


------------------------------------------------------------------------
r1696 | gaser | 2020-08-19 17:34:42 +0200 (Wed, 19 Aug 2020) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main1639.m
A       cat_main_clean_gwc1639.m
M       cat_main_updateSPM1639.m
M       html/cat.html

Changed: Added cat_main_clean_gwc1639 and calls from r1639 functions again.

------------------------------------------------------------------------
r1695 | gaser | 2020-08-19 16:59:49 +0200 (Wed, 19 Aug 2020) | 14 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_conf_long.m
M       cat_conf_tools.m
M       cat_roi_fun.m
M       html/cat.html
M       html/cat_starting.html
M       html/cat_versions.html

(1) Changed: Updated online help and CAT12 manual.
(2) Changed: Added more explanation used units for mean ROI function.

------------------------------------------------------------------------
r1694 | dahnke | 2020-08-19 15:42:00 +0200 (Wed, 19 Aug 2020) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_main1639.m
M       cat_main_amap.m
 M      cat_main_amap1639.m
D       cat_main_clean_gwc1639.m
M       cat_main_updateSPM1639.m

(1) Deleted:   Removed cat_main_clean_gwc1639 and replaced all calls in
               cat_main1639 and cat_main_updateSPM1639.
(2) Fixed:     Corrected definition of AMAP input segmentation in
               cat_main_amap.



------------------------------------------------------------------------
r1693 | gaser | 2020-08-19 14:41:36 +0200 (Wed, 19 Aug 2020) | 11 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cat_main1639.m
A       cat_main_amap1639.m
M       cat_run_job.m

(1) Changed: Replaced cat_main_amap in cat_main1639.m
(2) Added:   Added cat_main_amap1639.m from r1639 release.
(3) Changed: Updated Makefile.

------------------------------------------------------------------------
r1692 | dahnke | 2020-08-17 16:14:23 +0200 (Mon, 17 Aug 2020) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_main1639.m
M       cat_main_gintnorm.m
M       cat_main_gintnorm1639.m
M       cat_main_reportfig.m
M       cat_run_job.m
M       cat_run_job1639.m
M       cat_vol_partvol1639.m

(1) Changed:   Updated warnings in cat_run_job1639, car_main1639,
               cat_main_gintnorm1639, and cat_vol_partvol1639.


------------------------------------------------------------------------
r1691 | gaser | 2020-08-17 08:37:23 +0200 (Mon, 17 Aug 2020) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main1639.m
A       cat_main_clean_gwc1639.m
M       cat_main_updateSPM1639.m
M       html/cat.html

(1) Changed: Added calss to cat_main_clean_gwc1639 for r1639 stream.
(2) Added:   Rescued cat_main_clean_gwc1639.m from r1639.

------------------------------------------------------------------------
r1690 | gaser | 2020-08-14 15:35:42 +0200 (Fri, 14 Aug 2020) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_stat_check_cov.m
M       html/cat.html

(1) Changed: Again added check for new options for cat_stat_check_cov.m to show
             filenames and prefer boxplot.
(2) Changed: Updated release name.

------------------------------------------------------------------------
r1689 | gaser | 2020-08-14 15:30:29 +0200 (Fri, 14 Aug 2020) | 38 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
MM      cat12.sh
M       cat_batch_long.sh
M       cat_conf_tools.m
M       cat_long_main.txt
M       cat_long_mainShoot.txt
MM      cat_main1639.m
MM      cat_main_LAS21639.m
MM      cat_main_gintnorm1639.m
M       cat_main_reportfig.m
MM      cat_main_updateSPM1639.m
MM      cat_run_job1639.m
M       cat_spm_shoot_template.m
M       cat_stat_check_cov.m
M       cat_vol_defs.m
MM      cat_vol_partvol1639.m
M       check_pipeline_homogeneity.m
M       html/cat.html
 M      html/cat_methods_warnings.html
M       templates_volumes/cobra.nii

(1) Changed: Extended check_pipeline_homogeneity.m to check homogenity for each
             data set separetely.
(2) Changed: Simplified call for composite deformations in cat_vol_defs.m
(3) Changed: Added warning if not enough files were selected for longitudinal
             processing with cat_batch_long.sh.
(4) Fixed:   Call to spm_diffeo from oldSPM12 versions is now catched in
             cat_spm_shoot_template.m.
(5) Fixed:   Added new bounding box and voxel size options to longitudinal
             pipeline files.
(6) Changed: Updated checklist for Makefile.
(7) Changed: Added check for new options for cat_stat_check_cov.m tp show
             filenames and prefer boxplot.


------------------------------------------------------------------------
r1688 | gaser | 2020-08-12 14:04:07 +0200 (Wed, 12 Aug 2020) | 20 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.sh
M       cat_conf_tools.m
M       cat_io_cprintf.m
M       cat_run.m
M       cat_run_job.m
R       cat_run_job1639.m
M       cat_vol_defs.m
M       check_pipeline.sh
M       check_pipeline_homogeneity.m
M       html/cat.html

(1) Changed: check_pipeline_homogeneity.m now automatically saves png-images.
(2) Changed: Warnings for linking files will be suppressed in check_pipeline.sh.
(3) Changed: Added options for bounding box and voxel size to deformation tools.
(4) Changed: Suppress warnings in cat_io_cprintf.m for control sequences.


------------------------------------------------------------------------
r1687 | dahnke | 2020-08-11 13:59:57 +0200 (Tue, 11 Aug 2020) | 11 lines

Changed paths:
M       CHANGES.txt
A       cat_main1639.m
A       cat_main_LAS21639.m
A       cat_main_gintnorm1639.m
A       cat_main_updateSPM1639.m
A       cat_run_job1639.m
A       cat_vol_partvol1639.m

(1)  New:      Added preprocessing versions of R1639.

------------------------------------------------------------------------
r1686 | dahnke | 2020-08-10 18:17:38 +0200 (Mon, 10 Aug 2020) | 33 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_io_addwarning.m
M       cat_io_cprintf.m
M       cat_main.m
M       cat_main_amap.m
M       cat_main_clean_gwc.m
M       cat_main_gintnorm.m
M       cat_main_reportfig.m
M       cat_main_write.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_newcatch.m
M       cat_vol_resize.m

(1)  Changed:   Reinitialize r1639 preprocessing functions due to unsolved
                problems in the current version that can be now accessed
                via the extopts.experimental flag.
                Added versions of cat_run_job, cat_main, cat_main_updateSPM,
                cat_main_LAS2, cat_vol_partvol that where called from cat_run
                and cat_run_newcatch.
(2)  Changed:   Correction of background/skull-stripping estimation.
(3)  Fixed:     Small corrections in cat_main_reportfig, cat_main_AMAP, and
                cat_main_write.
(4)  Fixed:     Corrected bug with background interpolation in cat_vol_resize
                in anonymized images.
(5)  Changed:   Add more red to the warning color to improve visibility.
(6)  Changed:   Small corrections in cat_io_addwarning command line output.
(7)  Fixed:     Correction in cat_main_clean_gwc for improved cleanup.


------------------------------------------------------------------------
r1685 | dahnke | 2020-08-07 17:05:22 +0200 (Fri, 07 Aug 2020) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_gintnorm.m
M       cat_vol_partvol.m

(1)  Fixed:    Corrected bug in cat_main_gintnorm.
(2)  Fixed:    Use new old cleanup only for normal resolution and T1 contrast in cat_main.
(3)  Fixed:    Corrected WMHC setting for non T1 contrast in cat_vol_partvol.


------------------------------------------------------------------------
r1684 | dahnke | 2020-08-07 14:54:16 +0200 (Fri, 07 Aug 2020) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_io_addwarning.m
M       cat_main.m
M       cat_main_LAS2.m
M       cat_main_gintnorm.m
M       cat_main_reportfig.m

(1)  Fixed:    Corrected bug in cat_main_LAS2 but there are still some contrast problems
               in specific constrasts.
(2)  Fixed:    Corrected new line setting in cat_io_addwarning and calling functions
               cat_main_gintnorm
(3)  Changed:  Small adaption in Yp0 colormap in report figure in cat_main_reportfig.

------------------------------------------------------------------------
r1683 | dahnke | 2020-08-06 22:45:48 +0200 (Thu, 06 Aug 2020) | 29 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_io_addwarning.m
M       cat_io_report.m
M       cat_main.m
M       cat_main_LAS2.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_run_job.m
M       cat_stat_marks.m
M       cat_vol_qa.m
A       html/cat_methods_warnings.html

(1)  Fixed:    Corrected naming of jpg error report.
(2)  Fixed:    Corrected bias estimation in cat_vol_qa.
(3)  Fixed:    Improved estimation of skull-stripping and high intensity
               background in cat_run_job.
(4)  Changed:  Switched to new "old" cleanup routine also in the standard
               processing in cat_main.
(5)  Changed:  Separated human affine parameters in XML in
               cat_vol_qa and cat_stat_marks.
(6)  Changed:  Small visual changes in cat_io_addwarning.
(7)  Changed:  Print warning ID in CAT report.
(8)  Changed:  Added final scaling of the local correction maps in LAS
               by the globally estimated values.
(9)  Changed:  Activated visibility of the resize batch for all GUI levels.


------------------------------------------------------------------------
r1682 | gaser | 2020-08-06 14:06:53 +0200 (Thu, 06 Aug 2020) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
A       cat12.sh
M       cat_batch_cat.sh
M       check_pipeline.sh
M       html/cat.html

(1) Added:   Added wrapper "cat12.sh" to call cat_batch_cat.sh with predefined
             set of defaults that can be changed
(2) Changed: Updated help texts in shell scripts and Makefile.


------------------------------------------------------------------------
r1681 | dahnke | 2020-08-05 21:17:48 +0200 (Wed, 05 Aug 2020) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_io_addwarning.m
M       cat_main_APRG.m
M       cat_main_roi.m
M       cat_run_job.m

(1)  Changed:     Reset large parts of cat_run_job because of ongoing problems.
                  Removed block that test different masks for SPM preprocessing.
(2)  Changed:     Small changes in cat_main_APRG.
(3)  Changed:     Added box design in cat_io_addwarning to improve visibility in
                  the log-file.
(4)  Fixed:       Corrected tiny bug in cat_main_roi.


------------------------------------------------------------------------
r1680 | gaser | 2020-08-05 13:04:49 +0200 (Wed, 05 Aug 2020) | 25 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_cat.m
M       cat_batch_long.m
M       cat_batch_spm.m
M       cat_io_addwarning.m
M       cat_io_volctype.m
M       cat_main.m
M       cat_parallelize.m
M       cat_run_job_APRGs.m
M       cat_stat_check_cov.m
M       cat_stat_marks.m
M       check_pipeline.sh
M       check_pipeline_homogeneity.m
M       html/cat.html

(1) Changed: Updated help text and comments.
(2) Changed: Added verb-flag to check_pipeline_homogeneity.m.
(3) Changed: Simplified check for verb-flag in cat_stat_check_cov.m.
(4) Changed: Supress warnings right before exiting matlab programs to prevent
             annoying warnings.
(5) Fixed:   Corrected some size checks in check_pipeline.sh.


------------------------------------------------------------------------
r1679 | dahnke | 2020-08-04 16:56:24 +0200 (Tue, 04 Aug 2020) | 96 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_long.m
M       cat_conf_stools.m
M       cat_io_addwarning.m
M       cat_io_cprintf.m
M       cat_io_report.m
M       cat_io_strrep.m
M       cat_io_volctype.m
M       cat_main.m
M       cat_main_APRG.m
M       cat_main_LAS2.m
M       cat_main_amap.m
M       cat_main_gintnorm.m
M       cat_main_kamap.m
M       cat_main_registration.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job_APP_init.m
M       cat_run_job_APRGs.m
M       cat_run_newcatch.m
M       cat_stat_check_cov.m
M       cat_stat_histth.m
M       cat_stat_marks.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_gyrification.m
M       cat_surf_parameters.m
M       cat_surf_vx2surf.m
M       cat_vol_ctype.m
M       cat_vol_qa.m
M       cat_vol_sanlm.m
M       html/cat_methods_vx2surf.html
M       tbx_cfg_cat.m

Major changes
(1)  Fixed:      Changed skull-stripping settings of the new modifiable
                 APRG version (2<gcutstr<3) in cat_main_APRG.
(2)  Changed:    Second development step of cat_surf_vx2surf function.
                 Added dependencies for cat_surf_vx2surf batch.
                 Updated batch definition in cat_conf_stools.
                 Added help HTML page.
(3)  Changed:    Updated definition and documentation of cat_io_addwarning.
(4)  Changed:    Added detection of high intensity background in cat_run_job
                 cat_main_updateSPM, cat_main_gintnorm, and cat_main_LAS2 to
                 avoid too strong thresholding of lower intensities that
                 is required to handle multiple normal backgrounds.
(5)  Changed:    Many changes to handle SPM preprocessing in cat_run_job.
(6)  Changed:    Added documentation and removed old already commented code
                 blocks in cat_main_gintnorm.
(7)  Changed:    Corrected background/CSF handling in to correct
                 problems with MP2Rage data and images with multiple backgrounds
                 such as resliced or averaged data (using cat_job_run parameter).
(8)  Changed:    Updated output of warnings in cat_surf_createCS and cat_main_amap.
(9)  Changed:    Updated warnings in cat_run_job, cat_main, cat_main_amap
                 and other sub-functions.
(10) Fixed:      Corrected dependencies in cat_run and tbx_cfg_cat for
                 longitudinal surface processing.
(11) Changed:    Updated cat_stat_histth threshold parameter and calls of this
                 function (cat_run_job, cat_run_job_APP_init, cat_run_job_APRGs,
                 to support independent low and high thresholds.
(12) Fixed:      Corrected handling of prior input in cat_run_job_APRGs.

Minor changes
(1)  Fixed:      Reset normalization of surface to No in cat_conf_stools.
(2)  Fixed:      Improved scaling of the original image in cat_main_reportfig.
                 Corrected print resolution to 300 dpi.
                 Added _inactive_ block to test visualization of the TPM with
                 the initial affine registration matrix (Affine0).
(3)  Fixed:      Corrected little bugs in cat_conf_extopts, cat_run, and
                 cat_main_reportstr.
(4)  Fixed:      Corrected bugs in cerebellar pipeline of cat_create_CS2.
(5)  Fixed:      Added color settings for warning function.
(6)  Fixed:      Added redefinition of surface setting in cat_conf_long
                 to avoid selection of fast pipelines.
(7)  Fixed:      Changed definition of data input for the surf_calc batch
                 in cat_conf_tools to support dependency selection of
                 Freesurfer surface data.
(8)  Changed:    Added try-block for blood vessel correction in cat_main.
(9)  Changed:    Use higher thresholds in cat_main_kamap to avoid MP2Rage problems.
(10) Changed:    Added jpg output in cat_io_report (error report).
(11) Changed:    Added verb field to suppress output in cat_stat_check_cov to
                 estimate covariance matrix without command line report.
                 Corrected bug in output definition.
(12) Fixed:      Corrected tiny naming bugs in cat_surf_gyrification.
(13) Fixed:      Corrected bugs in cat_surf_parameters.
(14) Changed:    Corrected typos in cat_stat_marks, cat_main_registration,
                 cat_io_strrep, cat_io_volctype.
(15) Changed:    Updated warning output in cat_main_reportstr.
(16) Changed:    Added log and jpg file to error directory.
(17) Changed:    Added further documentation of XML fields in cat_stat_marks.


------------------------------------------------------------------------
r1678 | gaser | 2020-08-04 15:27:50 +0200 (Tue, 04 Aug 2020) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_catsimple.m
M       cat_simple.m
M       html/cat.html
M       standalone/cat_standalone.sh
M       standalone/cat_standalone_resample.txt
M       standalone/cat_standalone_simple.txt

(1) Fixed:   Corrected data_surf field in standalone files and added atlases.
(2) Changed: Changed default filter size for volume smoothing in cat_simple to
             6mm.

------------------------------------------------------------------------
r1677 | gaser | 2020-08-03 14:55:28 +0200 (Mon, 03 Aug 2020) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_run_job.m
M       cat_surf_createCS.m
M       cat_surf_fun.m
MM      check_pipeline_homogeneity.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Changed: Added some more try-catch commands to catch some errors that were
             often found with piwik statistics.
(2) Changed: Updated help text.

------------------------------------------------------------------------
r1676 | gaser | 2020-07-31 16:45:25 +0200 (Fri, 31 Jul 2020) | 20 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main_reportfig.m
M       cat_surf_createCS.m
M       cat_vol_groupwise_ls.m
M       check_pipeline.sh
M       html/cat.html
 M      html/cat_methods_vx2surf.html
 M      html/images/cat_surf_vx2surf_evalGM.png
 M      html/images/cat_surf_vx2surf_smoothing.png
 M      html/images/cat_surf_vx2surf_vol-int-dist.png
M       spm_diffeo_old.c

(1) Changed: For calculation of average/median image during rigid registration
             the minimum instead of median is now used for the case of only two
             images.
(2) Fixed:   Flag useprior was not correctly recognized in cat_surf_createCS.m


------------------------------------------------------------------------
r1675 | gaser | 2020-07-30 14:52:28 +0200 (Thu, 30 Jul 2020) | 21 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_long.m
M       cat_stat_analyze_ROIs.m
M       cat_stat_check_cov.m
M       cat_surf_createCS.m
M       cat_vol_groupwise_ls.m
M       check_pipeline.sh
A       check_pipeline_homogeneity.m
M       html/cat.html

(1) Changed: Extended check_pipeline.sh for longitudinal data.
(2) Added:   New tool for checking sample homogeneity for check_pipeline data.
(3) Fixed:   Correction for negative values was always enabled in
             cat_vol_groupwise_ls.m.
(4) Fixed:   Corrected check for usepior option in cat_surf_createCS.m
(5) Fixed:   Output files are now always written in analysis folder in
             cat_stat_analyze_ROIs.m.
(6) Fixed:   Check for input options added in cat_batch_long.m

------------------------------------------------------------------------
r1674 | dahnke | 2020-07-09 15:48:27 +0200 (Thu, 09 Jul 2020) | 23 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_stools.m
M       cat_main_gintnorm.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m
M       cat_run.m
M       cat_run_job.m
M       cat_surf_vx2surf.m
A       html/cat_methods_vx2surf.html
A       html/images/cat_surf_vx2surf_evalGM.png
A       html/images/cat_surf_vx2surf_smoothing.png
A       html/images/cat_surf_vx2surf_vol-int-dist.png

(1)  Changed:    Added dependencies for cat_surf_vx2surf batch.
                 Updated batch definition in cat_conf_stools.
                 Added help HTML page.
(2)  Fixed:      Corrected little bugs in cat_conf_extopts, cat_run, and
                 cat_main_reportstr.
(3)  Commented:  Added documentation in cat_main_gintnorm.


------------------------------------------------------------------------
r1673 | dahnke | 2020-07-06 19:02:18 +0200 (Mon, 06 Jul 2020) | 57 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_opts.m
M       cat_conf_output.m
M       cat_defaults.m
M       cat_io_addwarning.m
M       cat_main.m
M       cat_main_APRG.m
M       cat_main_amap.m
M       cat_main_gintnorm.m
M       cat_main_kamap.m
M       cat_main_registration.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m
M       cat_main_write.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job_APP_SPMfinal.m
M       cat_run_job_APRGs.m
M       cat_surf_createCS.m
M       cat_vol_qa.m
M       tbx_cfg_cat.m

(1)  Changed:  Updated colormap definition to keep a jet thickness map
               in the open report figure (cat_main_reportfig).
(2)  Changed:  Removed opengl, (s)atlas, and LAB fields in cat_report.
(3)  Changed:  Modified position of useprior settings in cat_run_job.
(4)  Changed:  Added WHMC on default GUI to turn it off in case of problems
               in special contrasts (cat_conf_extopts).
(5)  Changed:  Heavy update of the cat_io_addwarning and it calls to support
               updates of T2/PD processing, to have 3 different warning levels
               and simplified output handling in preprocessing report.
(6)  Changed:  Tiny cleanups of cat_main_gintnorm.
(7)  Changed:  Added some adaptions for PD/T2 processing in cat_main_amap.
(8)  Fixed:    Corrected some tiny bugs in cat_main_updateSPM.
(9)  Fixed:    Added missing variable in cat_run_job with APP=none.
(10) Fixed:    Corrected bug in KAMAP pipeline where bias_fwhm>0 cause
               MATLAB crash.
(11) Fixed:    Corrected bugs due to changes in APP light and full pipeline.
(12) Fixed:    Corrected GM=CSF=WM=0 segmentation error in long pipeline that
               was related to the individual TPM.
(13) Fixed:    Corrected bug in cat_main_registration.
(14) Fixed:    Corrected dependencies for fast surface processing in tbx_cfg_cat.
(15) New:      Integrated output of transformation matrix and with output
               field on the expert GUI (cat_conf_output, cat_main_write,
               cat_main_registration, cat_defaults, tbx_cfg_cat).
(16) New:      Added updated version of APRG to expert GUI
               (cat_main_APRG, cat_conf_extopts).
(17) New:      Added SPM super parameter to default GUI (cat_conf_opts) that
               control biasfwhm, biasreg, samp, and tol and replace the two
               separate bias and accuracy parameter.
(18) New:      Added recoloring of modified variables in cat_main_reportstr.



------------------------------------------------------------------------
r1672 | dahnke | 2020-07-02 10:26:11 +0200 (Thu, 02 Jul 2020) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_main_updateWMHs.m

(1) Fixed:     Corrected bug of missing variable in case of WMHs.

------------------------------------------------------------------------
r1671 | dahnke | 2020-07-01 23:30:25 +0200 (Wed, 01 Jul 2020) | 21 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_output.m
M       cat_io_addwarning.m
M       cat_io_report.m
M       cat_main.m
M       cat_main_amap.m
M       cat_main_gintnorm.m
M       cat_main_registration.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m
M       cat_main_write.m
M       cat_run_job.m
M       cat_vol_qa.m

(1) Fixed:     Updated command line output in cat_main_updateSPM (unfinished).
(2) Changed:   Updated handling of preprocessing warnings (unfinished).
(3) Fixed:     Corrected use of affine registration in cat_main_registration
               and added longitudinal prior case.


------------------------------------------------------------------------
r1670 | gaser | 2020-06-30 17:08:07 +0200 (Tue, 30 Jun 2020) | 5 lines

Changed paths:
M       CHANGES.txt

Changed: Corrected CHANGES.txt

------------------------------------------------------------------------
r1669 | gaser | 2020-06-30 16:52:56 +0200 (Tue, 30 Jun 2020) | 17 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_main_gintnorm.m
M       cat_main_registration2.m
M       cat_run_job.m
M       cat_run_job_APRGs.m
M       cat_spm_preproc_run.m
M       cat_stat_spm2x.m
M       cat_surf_render.m
M       cat_surf_results.m
M       html/cat.html

Changed: Corrected CHANGES.txt

------------------------------------------------------------------------
r1668 | dahnke | 2020-06-30 15:53:19 +0200 (Tue, 30 Jun 2020) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main.m
M       cat_main_amap.m
M       cat_main_gintnorm.m
M       cat_main_updateSPM.m
M       cat_run_job.m
M       cat_vol_partvol.m

(1) Fixed:     Correct incorrect settings of ignoreError option.

------------------------------------------------------------------------
r1667 | dahnke | 2020-06-30 10:31:23 +0200 (Tue, 30 Jun 2020) | 28 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_main.m
M       cat_main_amap.m
M       cat_main_gintnorm.m
M       cat_main_registration2.m
M       cat_main_reportstr.m
M       cat_run_job.m
M       cat_surf_render2.m
M       cat_surf_vx2surf.m

(1) Fixed:     Corrected affine registration problems for input
               data with outliers in cat_run_job.
(2) New:       Added external calls of 'view' and 'clim' setting
               in cat_surf_render2.
(3) Changed:   Updated functions in cat_surf_vx2surf and its GUI
               in cat_conf_stools.
(4) Changed:   Updated handling of T2/PD data in cat_main,
               cat_main_gintnorm, and cat_main_amap.
(5) Fixed:     Tiny correction of affine-registration parameter in
               cat_main_registration2.
(6) Fixed:     Tiny corrections of parameter output in cat_main_reportstr.
(7) Changed:   Set ignoreErrors=2 and reoved extopts.INV flag in cat_defaults.



------------------------------------------------------------------------
r1666 | gaser | 2020-06-26 17:01:29 +0200 (Fri, 26 Jun 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_slice_overlay.m

Fixed: Option for automatically selecting slices w.r.t. found maxima was not
       always working.

------------------------------------------------------------------------
r1665 | gaser | 2020-06-26 17:00:18 +0200 (Fri, 26 Jun 2020) | 24 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_amap.m
M       cat_main_registration2.m
M       cat_stat_analyze_ROIs.m
M       cat_stat_check_SPM.m
M       cat_surf_results.m
M       cat_tst_cattest.m
M       cat_vol_createTPM.m
M       cat_vol_slice_overlay.m
M       standalone/cat_standalone.sh

(1) Changed: Updated cat_vol_slice_overlay.m to deal with inverse effects on
             log-scaled p-values.
(2) Fixed:   Automatic estimation of thresholds was not correct for already
             thresholded data with inverse effects in cat_surf_results.m.
(3) Fixed:   Calling of cat_stat_check_SPM without parameters wasn't working.
(4) Fixed:   Output arguments were not working standalone versions in
             cat_main_registration2.m
(5) Changed: Updated help texts.
(6) Changed: Largely updated cat_stat_analyze_ROIs.m with more interaction,
             output and options.

------------------------------------------------------------------------
r1664 | dahnke | 2020-06-23 18:32:34 +0200 (Tue, 23 Jun 2020) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_amap.m
M       cat_main_gintnorm.m
M       cat_main_updateSPM.m
M       cat_run_job.m
M       cat_surf_vx2surf.m

(1) Fixed:   Corrected AMAP bias_fwhm parameter in ignoreError
             pipeline that cause fatal MATLAB errors. Corrected
             test of initial tissue definition.
(2) Changed: Deactivated low resolution call of cat_main_gintnorm.
(3) Fixed:   Corrected bug with the background definition of the
             in ignoreError pipeline in the low resolution call
             of cat_main_gintnorm.
(4) Fixed:   Corrected bugs in ignoreError pipeline in cat_main_updateSPM.


------------------------------------------------------------------------
r1663 | gaser | 2020-06-23 16:57:40 +0200 (Tue, 23 Jun 2020) | 32 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_io_writenii.m
M       cat_long_createTPM.m
M       cat_main.m
M       cat_run.m
M       cat_simple.m
M       cat_spm_results_ui.m
M       cat_stat_check_SPM.m
D       cat_stat_spm_results_ui.m
        > moved to development/cat_stat_spm_results_ui.m
M       cat_surf_create_TPM_hull_surface.m
M       cat_surf_render.m
M       cat_tst_cattest.m
A  +    development/cat_stat_spm_results_ui.m
        > moved from cat_stat_spm_results_ui.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Changed: Inverse contrasts are now only added for T-test in
             cat_spm_results_ui.m
(2) Fixed:   Corrected smaller bugs in cat_stat_check_SPM.m and
             cat_spm_results_ui.m that were caused under rare circumstances.
             mixing up with similar cat_spm_results_ui. that should be rather
             used.
(3) Fixed:   Corrected bug in tbx_cfg_cat.m when cat_conf_catsimple couldn't be
             found.
(4) Fixed:   tpm folder in spm should not be used with capitals (thanks to
             Martin Domin for pointing to that issue).

------------------------------------------------------------------------
r1662 | dahnke | 2020-06-22 21:03:14 +0200 (Mon, 22 Jun 2020) | 22 lines

Changed paths:
M       CHANGES.txt
M       cat_io_report.m
M       cat_long_mainShoot.txt
M       cat_main.m
M       cat_main_amap.m
M       cat_main_gintnorm.m
M       cat_run_job.m

(1) Fixed:   Corrected error in cat_io_report.
(2) Fixed:   Use internal definition for old label map and
             updated call of cat_main_amap. Update AMAP
             parametrization for ignoreError pipeline.
(3) Fixed:   Corrected bias correction in ignoreErrors pipeline
             in cat_main_gintnorm. Tried to get more robust tissue
             peak estimation.
(4) Fixed:   Corrected Pref definition in cat_long_mainShoot.txt.
(5) Changed: Use faster single SPM preprocessing in cat_run_job
             now also in ignoreError case.
(6) Changed: Use low WMHCstr in ignoreError pipeline in cat_main.


------------------------------------------------------------------------
r1661 | dahnke | 2020-06-21 18:11:54 +0200 (Sun, 21 Jun 2020) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_io_writenii.m
M       cat_main.m
M       cat_main_amap.m
M       cat_main_gintnorm.m
M       cat_main_kamap.m
M       cat_main_reportstr.m
M       cat_run_job.m
M       cat_vol_partvol.m
M       tbx_cfg_cat.m

(1) Changed:    Different changes to avoid AMAP crash in the ignoreError pipeline.


------------------------------------------------------------------------
r1660 | dahnke | 2020-06-19 21:05:53 +0200 (Fri, 19 Jun 2020) | 34 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_opts.m
M       cat_main.m
M       cat_main_amap.m
M       cat_main_gintnorm.m
M       cat_main_registration.m
M       cat_main_registration2.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job_APRGs.m
M       cat_run_newcatch.m
M       cat_vol_partvol.m
M       cat_vol_qa.m
M       tbx_cfg_cat.m

(1) Fixed:    Added update of the affine registration of the final
              segmentation in cat_main_registration.
(2) New:      Prepared a new while loop that allows to test different
              segmentation settings to avoid errors due to in-optimal
              input definitions, e.g., by using a improper background
              mask (changes in cat_run_job).
(3) New:      Added two additional flags to extopts.ignoreErrors that
              allows to run critical CAT functions and ignore warnings
              and errors that cause all other changes.
(4) Changed:  Corrected dependencies in case of fast surface reconstruction
              in tbx_cfg_cat.



------------------------------------------------------------------------
r1659 | gaser | 2020-06-19 11:44:29 +0200 (Fri, 19 Jun 2020) | 47 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_amap.mexa64
M       cat_amap.mexw64
M       cat_main_roi.m
M       cat_ornlm.mexa64
M       cat_ornlm.mexw64
M       cat_sanlm.mexa64
M       cat_sanlm.mexw64
MM      cat_surf_vx2surf.m
M       cat_vbdist.mexa64
M       cat_vbdist.mexw64
M       cat_vol_downcut.mexa64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.mexa64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.mexa64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mexa64
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mexa64
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.mexa64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mexa64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexa64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexa64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexa64
M       cat_vol_median3c.mexw64
M       cat_vol_pbtp.c
M       cat_vol_pbtp.mexa64
M       cat_vol_pbtp.mexmaci64
M       cat_vol_pbtp.mexw64
M       cat_vol_simgrow.mexa64
M       cat_vol_simgrow.mexw64
M       html/cat.html

(1) Changed: Changed space for estimating ROI volumes to native space because
             this gave better overlap to original volumes.
(2) Changed: Changed some settings in cat_vol_pbtp.c and recompiled that file.
(3) Changed: Added support for precompiled Linux version.

------------------------------------------------------------------------
r1658 | gaser | 2020-06-18 15:50:11 +0200 (Thu, 18 Jun 2020) | 23 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_amap.mexmaci64
M       cat_conf_stools.m
M       cat_main_gintnorm.m
M       cat_main_reportfig.m
M       cat_main_updateSPM.m
M       cat_run_job.m
M       cat_sanlm.mexmaci64
M       cat_vol_median3.mexmaci64
M       cat_vol_median3c.mexmaci64
M       cat_vol_pbtp.c
M       cat_vol_pbtp.mexmaci64
M       cat_vol_pbtp2.mexmaci64
M       html/cat.html

(1) Changed: Added try/catch to part of cat_main_reportfig.m where the main
             window often seems to be closed by some users.
(2) Changed: Updated help text and comments.
(3) Fixed:   Partially rescued settings for cat_vol_pbtp.c from r155x where
             thickness estimation was more accurate.

------------------------------------------------------------------------
r1657 | dahnke | 2020-06-17 13:15:21 +0200 (Wed, 17 Jun 2020) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_main_updateSPM.m
M       cat_run_job.m
M       cat_surf_vx2surf.m

(1) Fixed:    Added further correction in cat_main_updateSPM.
(2) Changed:  Added another try-catch layer in cat_run_job to
              handle errors in the initial segmentation.
(3) Fixed:    Corrected background definition bug in case of
              skull-stripped data in cat_main_updateSPM.


------------------------------------------------------------------------
r1656 | dahnke | 2020-06-16 11:06:52 +0200 (Tue, 16 Jun 2020) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_main.m
M       cat_main_roi.m
M       cat_main_write.m
M       cat_run_job.m
A       cat_surf_vx2surf.m

(1) Fixed:    Corrected push/pull settings in cat_main_roi.
(2) Changed:  Some further comments.
(3) New:      Prepared a batch and function to map voxel value to the surface
              by push/pull operations cat_surf_vx2surf.



------------------------------------------------------------------------
r1655 | gaser | 2020-06-15 13:45:57 +0200 (Mon, 15 Jun 2020) | 24 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_io_writenii.m
D       cat_long_main.m
        > moved to cat_long_main.txt
A  +    cat_long_main.txt
        > moved from cat_long_main.m
D       cat_long_mainShoot.m
        > moved to cat_long_mainShoot.txt
A  +    cat_long_mainShoot.txt
        > moved from cat_long_mainShoot.m
M       cat_long_multi_run.m
M       cat_main_roi.m
M       cat_run_job.m
M       html/cat.html

(1) Changed: ROI estimation again changed to template space in cat_main_roi.m.
(2) Fixed:   Longitudinal segmentation in deployed mode now uses a txt-file
             for the batch jobs to prevent that matlab files are compiled and
             therefore not readable by spm_jobman.m
(3) Fixed:   Corrected typos...

------------------------------------------------------------------------
r1654 | dahnke | 2020-06-14 20:31:14 +0200 (Sun, 14 Jun 2020) | 30 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_io_writenii.m
M       cat_main.m
M       cat_main_gintnorm.m
M       cat_main_registration.m
M       cat_main_roi.m
M       cat_main_updateSPM.m
M       cat_main_write.m
M       cat_run_job.m
M       cat_vol_qa.m

(1) Changed:   Increase ROI for SPM US estimation in cat_run_job that
               use the inverse of a 15 mm eroded background segment.
(2) Changed:   Use the 15 mm eroded background segment from cat_run_job
               in cat_main_updateSPM to reduce problems in regions
               without TPM definition.
(3) Changed:   Updated handling of SPM preprocessing problems with
               more detailed and interactive error message in cat_run_job
               and cat_main_gintnorm.
(4) Fixed:     Corrected bug in ICR estimation that applied signal
               intensity correction twice and result in to good values.
(5) Changed: 	 Added CAT version and revision to description of
               processed images.
(6) Changed:   Removed old interpolation of the deformation that was used
               to improve the push operation in cat_main_registration,
               cat_main_roi and cat_io_writenii.


------------------------------------------------------------------------
r1653 | gaser | 2020-06-12 17:02:05 +0200 (Fri, 12 Jun 2020) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_parameters.m
M       check_pipeline/batch_surface_pipeline.m
M       html/cat.html

(1) Changed: Deselected normalization option for extracting surface parameters.
(2) Changed: Updated batch_surface_pipeline.m

------------------------------------------------------------------------
r1652 | gaser | 2020-06-12 15:57:55 +0200 (Fri, 12 Jun 2020) | 9 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_conf_long.m
M       html/cat.html

Changed: Updated help text and CAT12 manual.

------------------------------------------------------------------------
r1651 | gaser | 2020-06-12 14:39:55 +0200 (Fri, 12 Jun 2020) | 15 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cat_main.m
M       cat_main_gintnorm.m
M       cat_main_roi.m
M       cat_run_job.m
M       check_pipeline_ROIs.m

(1) Changed: Updated criterai fpr getting peaks in cat_main_gintnorm.m to a more
             conservative value.
(2) Changed: Changed plotting limits in check_pipeline_ROIs.m.
(3) Changed: Set calculation of ROI values to native space in cat_main_rois.m


------------------------------------------------------------------------
r1650 | gaser | 2020-06-11 12:51:31 +0200 (Thu, 11 Jun 2020) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_io_report.m
M       cat_main_LAS2.m
M       cat_main_gintnorm.m
MM      standalone/cat_standalone_segment_long.txt

(1) Changed: Added some more try/catch to ensure that ignoreErrors is running.
(2) Fixed:   Changed estimation of tissue peaks in cat_main_gintnorm.m that
             failed if multiple peaks were deviating too much for a single
             tissue.


------------------------------------------------------------------------
r1649 | dahnke | 2020-06-10 21:28:49 +0200 (Wed, 10 Jun 2020) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_main_roi.m

(1) Changed:   Update subject space estimation and interpolation
               option in cat_main_roi.


------------------------------------------------------------------------
r1648 | dahnke | 2020-06-10 13:14:47 +0200 (Wed, 10 Jun 2020) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_ROI.m
M       cat_conf_tools.m
M       cat_main_roi.m
M       cat_surf_scaling.m
M       cat_vol_createTPM.m
M       cat_vol_resize.m

(1) Fixed:     Corrected data type bugs in cat_vol_resize.
(2) Changed:   Cleanup of cat_main_roi with new debugging output.


------------------------------------------------------------------------
r1647 | gaser | 2020-06-09 17:57:01 +0200 (Tue, 09 Jun 2020) | 18 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_long_main.m
M       cat_long_mainShoot.m
M       cat_long_multi_run.m
M       html/cat.html
M       html/cat_starting.html
M       standalone/cat_standalone_segment_long.txt
M       tbx_cfg_cat.m

(1) Changed: Replaced global variables by setappdata/getappdata because this
             are not working properly in deployed mode.
(2) Fixed:   Corrected link to long. batch in quick start guide.
(3) Fixed:   Corrected help text in Makefile for precompiling.


------------------------------------------------------------------------
r1646 | gaser | 2020-06-08 15:14:06 +0200 (Mon, 08 Jun 2020) | 16 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cat_run_job.m
M       standalone/cat_standalone.sh
M       standalone/cat_standalone_resample.txt
M       standalone/cat_standalone_segment.txt
A       standalone/cat_standalone_segment_long.txt
M       tbx_cfg_cat.m

(1) Changed: Added new standalone batch for longitudinal data.
(2) Changed: Updated standalone batches to consider new flags.
(3) Fixed:   Removed typo in cat_run_job.m that caused crash
(4) Fixed:   Removed try/catch error in tbx_cfg_cat.m


------------------------------------------------------------------------
r1645 | gaser | 2020-06-08 12:22:18 +0200 (Mon, 08 Jun 2020) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_run_job.m
M       tbx_cfg_cat.m

(1) Changed: XML label output for batch has ocasionally some issues for checking
             ROImenu structure.
(2) Changed: Supress warning for creating existing directories in cat_run_job.m.
(3) Changed: Updated help text in cat_conf_tools.m and again removed hidden flag
             for longitudinal registration.


------------------------------------------------------------------------
r1644 | dahnke | 2020-06-07 19:02:53 +0200 (Sun, 07 Jun 2020) | 30 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_long_mainShoot.m
M       cat_long_multi_run.m
M       cat_main_roi.m
M       cat_run_job.m
M       cat_vol_createTPM.m
M       cat_vol_headtrimming.m
M       cat_vol_resize.m
M       spm_cat12.m
M       tbx_cfg_cat.m

(1) New:      Update cat_vol_resize and the resize batch to use volume
							properties of another image.  In contrast to imcalc also
							the first 3 dimensions of additional n-dimensional
							components are resized.
(2) New:		  Added parameter to control application of deformation in
              the longitudinal pipeline.
(3) Changed:  Restructured TPM creation pipeline focusing on Shooting
							input as far as this is the core routine to normalized
							data of another cohort. Updated batch GUI in cat_conf_tools.
(4) Fixed:		Corrected rare bug in cat_main_registration.
(5) Fixed: 		Corrected bugs in cat_main_roi if no atlas is available
							and incorrect volume estimation for specific combinations
							of atlas, template and image resolution.
(6) Fixed: 		Corrected bug in cat_vol_headtrimming.
(7) Changed: 	Added longmodel variable to cat_long_multi_mainShoot batch.


------------------------------------------------------------------------
r1643 | gaser | 2020-06-05 16:16:48 +0200 (Fri, 05 Jun 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat12.m

Changed: Again added (corrected) call to previous versions from CAT12 GUI


------------------------------------------------------------------------
r1642 | gaser | 2020-06-05 16:12:03 +0200 (Fri, 05 Jun 2020) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_vol_groupwise_ls.m

(1) Changed: Removed call to previous versions from CAT12 GUI:
(2) Changed: Changed output format for long. data to float32.

------------------------------------------------------------------------
r1641 | gaser | 2020-06-05 14:32:57 +0200 (Fri, 05 Jun 2020) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_long.m
M       cat_batch_long.sh
M       cat_conf_long.m
M       cat_long_createTPM.m
M       cat_long_multi_run.m
M       cat_vol_groupwise_ls.m

(1) Changed: Added option for longitudinal mode for detecting large changes.
(2) Changed: Updated batch scripts to consider new option for large changes.
(3) Fixed:   Prevent negative values in longitudinal registration after
             intra-subject bias correction.

------------------------------------------------------------------------
r1640 | gaser | 2020-06-04 17:50:51 +0200 (Thu, 04 Jun 2020) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_ROI.m
M       cat_conf_long.m
M       cat_conf_output.m
M       cat_conf_stools.m
M       cat_long_main.m
M       cat_long_mainShoot.m
M       cat_long_multi_run.m
M       html/cat.html

(1) Changed: Removed sROI menu from pipeline.
(2) Changed: Added sROI option to extract ROI function for surfaces.

------------------------------------------------------------------------
r1639 | gaser | 2020-06-04 12:47:03 +0200 (Thu, 04 Jun 2020) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m
M       tbx_cfg_cat.m

(1) Changed: Check successful loading of previous CAT12 versions and skip GUI
             entries if any problems occur.
(2) Fixed:   Corrected deletion of thickness data if debugging was enabled.

------------------------------------------------------------------------
r1638 | gaser | 2020-05-29 16:52:39 +0200 (Fri, 29 May 2020) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_long_mainShoot.m
MM      cat_long_shoot_defaults.m
MM      cat_spm_shoot_template.m
 M      cat_vol_createTPM.m

Fixed: Last file deletions in longitudinal pipeline were not yet working.


------------------------------------------------------------------------
r1637 | gaser | 2020-05-28 17:09:16 +0200 (Thu, 28 May 2020) | 25 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_ROI.m
M       cat_conf_tools.m
M       cat_long_mainShoot.m
M       cat_plot_boxplot.m
M       cat_run.m
M       cat_stat_analyze_ROIs.m
M       check_pipeline.sh
M       check_pipeline_ROIs.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Changed: Updated longitudinal pipeline
(2) Changed: Updated server name in check_pipeline.sh
(3) Changed: Unset hidden flag for longitudinal registration.
(4) Fixed:   Dependency for ROI output was not working.
(5) Fixed:   check_pipeline_ROIs was not correctly dealing with csv without
             header.
(6) Fixed:   Check for missing ROI xml files was not working.
(7) Fixed:   Non-cell data in cat_plot_boxplot.m were not correctly converted
             to cell data.


------------------------------------------------------------------------
r1636 | dahnke | 2020-05-25 20:07:09 +0200 (Mon, 25 May 2020) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_ROI.m
MM      cat_long_mainShoot.m
M       spm_cat12.m

(1) Fixed:   Corrected surface ROI batch definition in cat_conf_ROI and spm_cat12.
(2) Fixed:	 Corrected deletion of shooting files in long batch.

------------------------------------------------------------------------
r1635 | gaser | 2020-05-25 00:38:28 +0200 (Mon, 25 May 2020) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_long_mainShoot.m
A       cat_long_shoot_defaults.m
A       cat_spm_shoot_template.m
MM      cat_surf_map_atlas.m
A       cat_vol_createTPM.m

(1) Fixed:   Added missing files for new longitudinal batch mode.
(2) Changed: Removed correction of segmentation field in cat_long_mainShoot.m
(3) Changed: Updated help texts in new functions and corrected typos.

------------------------------------------------------------------------
r1634 | dahnke | 2020-05-22 20:31:12 +0200 (Fri, 22 May 2020) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_long.m
M       cat_conf_output.m
M       cat_conf_tools.m
A       cat_long_mainShoot.m
M       cat_long_multi_run.m
M       cat_surf_fun.m
M       cat_vol_qa.m
M       cat_vol_resize.m

(1) Fixed:     Corrected longitudinal batch definition.
(2) New:       Added general create TPM batch.
(3) Changed:   Hid longitudinal create TPM and realign batches.
(4) New:       Added batch to resize images and update cat_vol_resize.


------------------------------------------------------------------------
r1633 | gaser | 2020-05-20 17:00:04 +0200 (Wed, 20 May 2020) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_spm2x.m
R       cat_surf_map_atlas.m
M       cat_surf_max.m
M       cat_surf_parameters.m
M       cat_surf_scaling.m
M       check_pipeline/batch_volume_pipeline.m

(1) Changed: Added some more suppressions of annoying subscript warnings.
(2) Fixed:   Field for Toro-GI was not correctly set in cat_surf_parameters.m


------------------------------------------------------------------------
r1632 | gaser | 2020-05-20 14:57:05 +0200 (Wed, 20 May 2020) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m

Fixed: OI estimation for surfaces was skipped in cat_main.m

------------------------------------------------------------------------
r1631 | gaser | 2020-05-20 09:59:07 +0200 (Wed, 20 May 2020) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       html/cat.html

Fixed: We still have to use the differentiation between different modes because
       the developersettings for surf2roi are not yet working

------------------------------------------------------------------------
r1630 | gaser | 2020-05-19 16:53:30 +0200 (Tue, 19 May 2020) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_output.m
M       cat_long_main.m
M       cat_vol_maskimage.m

(1) Changed: Removed expert-call in long. batch mode which is not needed
             anymore.
(2) Fixed:   Corrected weird bug in cat_conf_tools.m that caused crash of SPM
             batch system.


------------------------------------------------------------------------
r1629 | gaser | 2020-05-19 12:45:05 +0200 (Tue, 19 May 2020) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_long.m
M       cat_conf_stools.m
M       cat_main_reportfig.m
M       cat_main_roi.m
M       cat_spm_results_ui.m
M       cat_stat_results.m
M       tbx_cfg_cat.m

(1) Changed: Updated some hidden flags and unified use of numcores and nproc in
             config files.
(2) Fixed:   Corrected some calls to functions/options that often crashed
             according to piwik analysis
(3) Fixed:   Corrected (wrong) calls to cat_stat_spm_results*


------------------------------------------------------------------------
r1628 | gaser | 2020-05-18 12:52:46 +0200 (Mon, 18 May 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_groupwise_ls.m

Fixed: Corrected bug in cat_vol_groupwise_ls.m for non-linear registration
       where a variable was overwritten.

------------------------------------------------------------------------
r1627 | gaser | 2020-05-18 12:50:08 +0200 (Mon, 18 May 2020) | 9 lines

Changed paths:
M       CHANGES.txt
A  +    cat_surf_map_atlas.m
M       cat_vol_groupwise_ls.m

(1) Fixed: Corrected false deletion of cat_surf_map_atlas.m
(2) Fixed: Corrected bug in cat_vol_groupwise_ls.m for non-linear registration
           where a variable was overwritten.

------------------------------------------------------------------------
r1626 | gaser | 2020-05-18 00:17:00 +0200 (Mon, 18 May 2020) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_long.m
M       cat_conf_stools.m
M       cat_long_multi_run.m
D       cat_surf_map_atlas.m
M       tbx_cfg_cat.m

Fixed: Corrected ROI menus for long. mode.


------------------------------------------------------------------------
r1625 | dahnke | 2020-05-17 16:04:25 +0200 (Sun, 17 May 2020) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_long.m
M       cat_conf_output.m
M       cat_long_main.m
MM      cat_surf_map_atlas.m
M       tbx_cfg_cat.m

(1) Fixed:  Corrected small bugs with wrong fields in longitudinal GUI.
(2) New:    Added surface atlas element to the longitudinal GUI.


------------------------------------------------------------------------
r1624 | dahnke | 2020-05-16 16:51:13 +0200 (Sat, 16 May 2020) | 22 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_output.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_io_report.m
M       cat_long_createTPM.m
M       cat_run.m
M       cat_surf_create_TPM_hull_surface.m
D       html/vbm_vol_correct_slice_scaling_768.png
M       tbx_cfg_cat.m
M       templates_animals/chimpanzee_TPM.nii
M       templates_surfaces/bh.headbrain.TPM.gii

(1) New:			Added dependencies for TPM output.
(2) Changed:	Use hidden field to avoid GUI elements on simpler
							GUI levels rather than to avoid creation.
(3) New:			Added another TPM level with smaller smoothing.
(4) Fixed: 		Corrected small bug in cat_surf_create_TPM_hull_surface.
(5) Fixed:		Corrected bug in naming the error output files in cat_io_report.

------------------------------------------------------------------------
r1623 | gaser | 2020-05-15 18:10:02 +0200 (Fri, 15 May 2020) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_run_job.m

Fixed: Prior for long. batch was sometimes using wrong folder.

------------------------------------------------------------------------
r1622 | gaser | 2020-05-15 15:18:40 +0200 (Fri, 15 May 2020) | 19 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
MM      cat_long_createTPM.m
M       cat_long_main.m
 M      cat_stat_results.m
MM      cat_stat_spm_results_ui.m
A       cat_surf_map_atlas.m
M       html/cat.html

(1) Changed: Added new function to map Freesurfer annot atlas labels to
             individual surfaces: cat_surf_map_atlas.m
(2) Changed: Updated Resampling function CAT_ResampleSurf to support label
             interpolation.
(3) Changed: Compiled all CAT*c files to consider new changes.
(4) Changed: Updated new long. mode and integrated new function to use long
             TPMs.

------------------------------------------------------------------------
r1621 | gaser | 2020-05-14 17:30:16 +0200 (Thu, 14 May 2020) | 23 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_long.m
M       cat_batch_long.sh
M       cat_conf_long.m
M       cat_long_main.m
M       cat_long_multi_run.m
M       cat_main_reportfig.m
M       cat_surf_parameters.m
M       cat_vol_approx.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Changed: Reordered and removed some items in tbx_cfg_cat.m.
(2) Changed: Headless mode without will not allow printing pdf/jpg report.
(3) Changed: Added selection options for longitudinal mode for subjects and
    time points (borrowed from simple long. processing).
(4) Changed: Many changes in longitudinal batch.
(5) Fixed: Disabled dependencies for long. batch because it's not yet working.
(6) Changed: Updated shell and batch for longitudinal processing from command
    line.

------------------------------------------------------------------------
r1620 | dahnke | 2020-05-14 15:59:40 +0200 (Thu, 14 May 2020) | 89 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_io_rerun.m
M       cat_io_volctype.m
M       cat_io_xml.m
A       cat_long_createTPM.m
M       cat_main.m
M       cat_main_LAS2.m
M       cat_main_registration.m
M       cat_main_reportfig.m
M       cat_main_roi.m
M       cat_main_updateSPM.m
M       cat_parallelize.m
M       cat_run.m
M       cat_run_job.m
M       cat_stat_histth.m
A       cat_stat_results.m
A       cat_stat_spm_results_ui.m
M       cat_surf_calc.m
M       cat_surf_createCS.m
M       cat_surf_create_TPM_hull_surface.m
M       cat_surf_display.m
M       cat_surf_fun.m
M       cat_surf_gyrification.m
M       cat_surf_info.m
M       cat_surf_parameters.m
M       cat_surf_render2.m
M       cat_surf_resamp.m
M       cat_surf_scaling.m
M       cat_vol_approx.m
M       cat_vol_qa.m
M       tbx_cfg_cat.m
!       templates_animals/chimpanzee_TPM.nii
M       templates_animals/chimpanzee_cat.nii

(1)  New:			Added cat_stat_spm_run_results.m to support batch call of
							cat_surf_spm_results_ui.m. Added batch definition in
							cat_conf_stools.m:line 99-168 that only update the
							dependencies from volume to surface type.
(2)  Removed: Replaced cat_io_lazy.m by cat_io_rerun.m that is used to check
							if a file needs to be reprocessed (in the lazy mode) because
							the input file has changed.
(3)  Changed: Added warning in case of negative input images that can cause
							preprocessing problems.
(4)  Changed: Removed fix texture clims in cat_surf_display.
(5)	 Changed:	Improved handling of mixed and separated data input for the
			 				resample and smooth batch to handle dependencies correctly in
			 				cat_conf_stools.m>cat_surf_resamp_GUI:937-964 and dependencies in
			 				cat_conf_stools.m>cat_surf_resamp:185#-197# and cat_surf_resamp.
(6)  Changed: Updated surface parameter GUI with one single normalization
							parameter for all measures.
							cat_conf_stools.m>cat_surf_resmap_GUI:1188-14## and dependencies
						  cat_conf_stools.m>vout_cat_surf_results:16##-175#.
(7)  Changed: Switch to silent surface rendering in cat_surf_fun>cat_surf_surf2vol.
							Added case to call mesh interpolation subfunction cat_surf_fun>
							cat_surf_meshinterp.
(8)  Changed: Added lazy and intensity normalization parameter in cat_io_volctype
							and its batch definition in cat_conf_tools.
(9)  Fixed: 	Added error message in cat_io_xml in case of incorrect input.
(10) Fixed: 	Corrected progress counting problems in cat_parallelize.m.
(11) Fixed: 	Corrected smaller things in cat_surf_scaling.m.
(12) Fixed: 	Corrected bug in cat_surf_calc.
(13) Fixed: 	Corrected bug in cat_main in case of fast surface reconstruction without
              registration that do not allow surface-based ROI analysis.
(14) Fixed: 	Corrected small bugs in cat_main_roi.
(15) Fixed: 	Corrected bug in cat_main_registration that happen if no affine registration
							is used.
(16) Fixed:		Corrected some settings in cat_surf_gyrification (developer).
(17) Fixed: 	Corrected bug in cat_main_reportfig in case of missing pial/white surface.
(18) Fixed: 	Added current flags for cerebellar processing in cat_surf_createCS.
						 	Corrected some incorrect settings in case of negative images.
(19) Fixed:		Corrected handling of negative values in cat_vol_approx.
(20) Fixed: 	Corrected handling of folding measures in cat_surf_render2 and cat_surf_info.
(21) Fixed:		Corrected bug in cat_stat_histth in case of imaginary numbers.
(22) Fixed: 	Corrected some bugs in cat_vol_qa for smaller brains (primates).
(23) Fixed:		Corrected affine registration issue in non-human data.
(24) Fixed:		Corrected bugs in cat_io_rerun.
(25) Fixed:		Corrected XML dependency of the main preprocessing in tbx_cfg_cat
 							and cat_run.
(26) Fixed:   Corrected some bugs in cat_run.m:49-62 without parallel processing.
(27) New:			Added call of Schaer's GI in the developer mode for comparisons
							with other folding measures.
(28) Fixed:	  Corrected bug in case of TPMs with only 3 input classes by assuming that
              class 4 is the undefined background. Added also a warning.



------------------------------------------------------------------------
r1619 | gaser | 2020-05-14 08:02:27 +0200 (Thu, 14 May 2020) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_batch_long.m
M       cat_conf_catsimple.m
M       cat_conf_long.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_long_main.m
M       cat_simple.m
M       tbx_cfg_cat.m

(1) Changed: Moved call to cat_conf_long to tbx_cfg_cat.m to have it on the
    same level as straigh segmentation.
(2) Changed: Added term "(current release)" to CAT12 segmentation and
    longitudinal segmentation to indicate version.
(3) Changed: Updated help text

------------------------------------------------------------------------
r1618 | gaser | 2020-05-13 14:58:08 +0200 (Wed, 13 May 2020) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_defaults.m
M       cat_main.m
M       cat_main_write.m
M       cat_run.m
M       cat_surf_createCS.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Changed: Updated help text for using priors ofr long. data.
(2) Fixed: Corrected and extended dependencies in tbx_cfg_cat.m and cat_run.m.
(3) Fixed: Set useprior field in cat_main.m if not defined.

------------------------------------------------------------------------
r1617 | gaser | 2020-05-13 00:36:45 +0200 (Wed, 13 May 2020) | 20 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_tools.m
M       cat_long_main.m
M       cat_long_multi_run.m
M       cat_main.m
M       cat_run.m
M       cat_run_job.m
M       cat_surf_createCS.m
M       tbx_cfg_cat.m

(1) Changed: Added option to use estimated parameters of (average) image
    for using as prior for affine registration, segmentation and surface
    extraction.
(2) Changed: Modified longitudinal batch w.r.t. the use of prior information.
(3) Fixed: Corrected typos.
(4) Changed: Parallel mode is now disabled in longitudinal batch if only one
    subject is selected.

------------------------------------------------------------------------
r1616 | gaser | 2020-05-10 23:16:49 +0200 (Sun, 10 May 2020) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_groupwise_ls.m
M       html/cat_statistics.html

(1) Changed: Added visitor plot to CAT12 user statistic page.
(2) Changed: Use weighted average of mean and median w.r.t. local stdev for
    creating average image for rigid registration in longitudinal mode.

------------------------------------------------------------------------
r1615 | gaser | 2020-05-09 12:19:40 +0200 (Sat, 09 May 2020) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_main.m
M       cat_run.m

(1) Fixed: Dependencies for rigidly aligned data were missing the "_rigid" term.
(2) Fixed: Skip getting ROI values for fast versions of surface extraction.

------------------------------------------------------------------------
r1614 | gaser | 2020-05-08 16:39:49 +0200 (Fri, 08 May 2020) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_io_checkdepfiles.m
M       html/cat.html

(1) Changed: Added some remarks fro precompiling to Makefile
(2) Fixed: Prevented interpreting backslash as escape character in
    cat_io_checkdepfiles.m. Thanks to Brendan Balken for pointing to that issue.

------------------------------------------------------------------------
r1613 | gaser | 2020-05-04 19:36:07 +0200 (Mon, 04 May 2020) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_update.m
M       html/cat.txt

Changed: Update function skips use of spm('alert') because messages after
successful update were too long.

------------------------------------------------------------------------
r1612 | gaser | 2020-05-03 14:18:52 +0200 (Sun, 03 May 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_check_cov.m
M       cat_stat_check_cov2.m

Changed: Updated list of doubled and similar data in cat_stat_check_cov*.m

------------------------------------------------------------------------
r1611 | gaser | 2020-04-30 09:00:24 +0200 (Thu, 30 Apr 2020) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_resamp_freesurfer.m
M       html/cat.html

Fixed: Resampling for longitudinal Freesurfer data was not finding the correct
folder name.

------------------------------------------------------------------------
r1610 | gaser | 2020-04-29 18:49:12 +0200 (Wed, 29 Apr 2020) | 17 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_plot_boxplot.m
M       cat_spm_results_ui.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_results.m

(1) Fixed: Solved error with displaying surface ROI results in
    cat_surf_results.m.
(2) Fixed: Current directory of results was not considered in
    cat_spm_results_ui.m.
(3) Changed: Updated help text and CAT12 manual (contrasts for
    longitudinal designs with 2 groups).
(4) Fixed: In rare cases violinplot in cat_plot_boxplot.m failed.

------------------------------------------------------------------------
r1609 | gaser | 2020-04-21 22:38:40 +0200 (Tue, 21 Apr 2020) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_run.m
M       cat_spm_results_ui.m
M       html/cat.html

(1) Fixed: Removed dome inconsitencies in cat_spm_results_ui.m where existing
    TFCE results were initially not found.
(2) Fixed: Corrected incompatibiliy with older SPM12 versions in cat_run.m.

------------------------------------------------------------------------
r1608 | gaser | 2020-04-20 22:25:55 +0200 (Mon, 20 Apr 2020) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m
M       cat_stat_check_cov.m
M       cat_stat_check_cov2.m

(1) Fixed: Removed bug in cat_spm_results_ui.m where surface results could not
    be displayed.
(2) Changed: Added some more checks for missing or non-valid parameters in
    cat_stat_check_cov*.m

------------------------------------------------------------------------
r1607 | gaser | 2020-04-18 00:52:07 +0200 (Sat, 18 Apr 2020) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_spm2x.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_rgb_ui.m
M       cat_vol_slice_overlay_ui.m

(1) Fixed: Corrected bug in cat_stat_sp2x.m if no results were found and atlas
    function was enabed.
(2) Changed: Updated cat_vol_slice_overlay to automatically estimate filename
    for saving.
(3) Changed: Added helptext to cat_vol_slice_overlay*.m

------------------------------------------------------------------------
r1606 | gaser | 2020-04-14 21:24:35 +0200 (Tue, 14 Apr 2020) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat12.m

Fixed: Corrected bug with update function.

------------------------------------------------------------------------
r1605 | gaser | 2020-04-14 20:44:36 +0200 (Tue, 14 Apr 2020) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_output.m
M       html/cat.html
M       tbx_cfg_cat.m

Fixed: Corrected bug with (disabled) temporary version r1585.

------------------------------------------------------------------------
r1604 | gaser | 2020-04-14 14:39:10 +0200 (Tue, 14 Apr 2020) | 17 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_install_tfce.m
M       cat_io_send_to_server.m
M       cat_update.m
M       html/cat.html
M       html/cat_starting.html
M       html/cat_versions.html
M       tbx_cfg_cat.m

(1) Changed: Updated version information and online help.
(2) Changed: Removed temporary 1585 version from GUI.
(3) Changed: Updated server address.

------------------------------------------------------------------------
r1603 | gaser | 2020-04-13 02:12:27 +0200 (Mon, 13 Apr 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m

Fixed: Corrected bug with non-detectable call_list function in
cat_spm_results_ui.m

------------------------------------------------------------------------
r1602 | gaser | 2020-04-13 01:39:24 +0200 (Mon, 13 Apr 2020) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m

Fixed: Corrected some inconsistencies in cat_spm_results_ui.m.

------------------------------------------------------------------------
r1601 | gaser | 2020-04-13 00:22:54 +0200 (Mon, 13 Apr 2020) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_analyze_ROIs.m
M       standalone/cat_standalone.sh
RM      templates_volumes/aal3.csv
RM      templates_volumes/aal3.nii
RM      templates_volumes/aal3.txt

(1) Fixed: Corrected bug in ROI analysis that occured if only a few regions were
    found to be significant.
(2) Fixed: Removed unnecessary cell-structure in cat_standalone.sh

------------------------------------------------------------------------
r1600 | gaser | 2020-04-10 01:31:30 +0200 (Fri, 10 Apr 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m

Changed: Added check to cat_spm_results_ui if TFCE is installed (for general
use in CAT12).

------------------------------------------------------------------------
r1599 | gaser | 2020-04-10 01:18:34 +0200 (Fri, 10 Apr 2020) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
A  +    cat_spm_results_ui.m
        > moved from cat_stat_spm_results_ui.m
D       cat_stat_spm_results_ui.m
        > moved to cat_spm_results_ui.m

(1) Changed: Renamed cat_stat_spm_results_ui.m to cat_spm_results_ui.m and
    added functionality to optionally call TFCE results.
(2) Changed: Added option to call results to CAT12 GUI.

------------------------------------------------------------------------
r1598 | gaser | 2020-04-09 16:41:45 +0200 (Thu, 09 Apr 2020) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_io_matlabversion.m
M       cat_run1173plus/cat_conf_opts1173plus.m
M       cat_run_job.m
M       cat_run_newcatch.m
M       cat_spm_smoothto8bit.m
M       cat_surf_render.m
M       cat_surf_results.m
M       cat_vol_findfiles.m
MM      internal/cat_io_send_udp_to_server.m
M       tbx_cfg_cat.m

(1) Changed: Made some function compatible to Octave.
(2) Changed: Changed some of the defaults for displaying surfaces with
    cat_surf_render.m (transparency, texture, crossbar).

------------------------------------------------------------------------
r1597 | gaser | 2020-04-09 00:44:32 +0200 (Thu, 09 Apr 2020) | 31 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
 M      atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot
 M      atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot
 M      atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot
 M      atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot
 M      atlases_surfaces/rh.Schaefer2018_100Parcels_17Networks_order.annot
 M      atlases_surfaces/rh.Schaefer2018_200Parcels_17Networks_order.annot
 M      atlases_surfaces/rh.Schaefer2018_400Parcels_17Networks_order.annot
 M      atlases_surfaces/rh.Schaefer2018_600Parcels_17Networks_order.annot
M       html/cat.html
M       html/cat_methods_FN.html
M       html/cat_starting.html
M       html/style.css
 M      templates_volumes/Schaefer2018_100Parcels_17Networks_order.csv
 M      templates_volumes/Schaefer2018_100Parcels_17Networks_order.nii
 M      templates_volumes/Schaefer2018_200Parcels_17Networks_order.csv
 M      templates_volumes/Schaefer2018_200Parcels_17Networks_order.nii
 M      templates_volumes/Schaefer2018_400Parcels_17Networks_order.csv
 M      templates_volumes/Schaefer2018_400Parcels_17Networks_order.nii
 M      templates_volumes/Schaefer2018_600Parcels_17Networks_order.csv
 M      templates_volumes/Schaefer2018_600Parcels_17Networks_order.nii
 M      templates_volumes/aal3.csv
 M      templates_volumes/aal3.nii
MM      templates_volumes/aal3.txt

(1) Changed: Updated help site for naming convention of output files.
(2) Changed: Updated Makefile.

------------------------------------------------------------------------
r1596 | gaser | 2020-04-07 20:25:35 +0200 (Tue, 07 Apr 2020) | 29 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_amap.mex
M       cat_ornlm.mex
M       cat_sanlm.mex
M       cat_vbdist.mex
M       cat_vol_downcut.mex
M       cat_vol_eidist.mex
M       cat_vol_genus0.mex
M       cat_vol_gradient3.mex
M       cat_vol_interp3f.mex
M       cat_vol_laplace3.mex
M       cat_vol_laplace3R.mex
M       cat_vol_localstat.mex
M       cat_vol_median3.mex
M       cat_vol_median3c.mex
M       cat_vol_pbtp.mex
M       cat_vol_simgrow.mex
M       html/cat.html
A       internal/cat_io_send_udp_to_server.m
M       internal/cat_vol_cMRegularizarNLM3D.mex
M       spm_cat12.m

(1) Added: Internal tool to send udp information.
(2) Changed: Updated cat12.m and spm_cat12.m to be more conform across
    different systems.

------------------------------------------------------------------------
r1595 | gaser | 2020-03-31 14:33:37 +0200 (Tue, 31 Mar 2020) | 100 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       atlases_surfaces/atlases_surfaces.man
A       atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot
A       atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot
A       atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot
A       atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot
A       atlases_surfaces/rh.Schaefer2018_100Parcels_17Networks_order.annot
A       atlases_surfaces/rh.Schaefer2018_200Parcels_17Networks_order.annot
A       atlases_surfaces/rh.Schaefer2018_400Parcels_17Networks_order.annot
A       atlases_surfaces/rh.Schaefer2018_600Parcels_17Networks_order.annot
M       atlases_surfaces_32k/atlases_surfaces_32k.man
D       atlases_surfaces_32k/lh.Schaefer2018_1000Parcels_17Networks_order.annot
        > moved to atlases_surfaces_not_distributed/lh.Schaefer2018_1000Parcels_17Networks_order.annot
D       atlases_surfaces_32k/lh.Schaefer2018_1000Parcels_7Networks_order.annot
        > moved to atlases_surfaces_not_distributed/lh.Schaefer2018_1000Parcels_7Networks_order.annot
D       atlases_surfaces_32k/lh.Schaefer2018_100Parcels_7Networks_order.annot
        > moved to atlases_surfaces_not_distributed/lh.Schaefer2018_100Parcels_7Networks_order.annot
D       atlases_surfaces_32k/lh.Schaefer2018_200Parcels_7Networks_order.annot
        > moved to atlases_surfaces_not_distributed/lh.Schaefer2018_200Parcels_7Networks_order.annot
D       atlases_surfaces_32k/lh.Schaefer2018_400Parcels_7Networks_order.annot
        > moved to atlases_surfaces_not_distributed/lh.Schaefer2018_400Parcels_7Networks_order.annot
D       atlases_surfaces_32k/lh.Schaefer2018_600Parcels_7Networks_order.annot
        > moved to atlases_surfaces_not_distributed/lh.Schaefer2018_600Parcels_7Networks_order.annot
D       atlases_surfaces_32k/lh.Schaefer2018_800Parcels_17Networks_order.annot
        > moved to atlases_surfaces_not_distributed/lh.Schaefer2018_800Parcels_17Networks_order.annot
D       atlases_surfaces_32k/lh.Schaefer2018_800Parcels_7Networks_order.annot
        > moved to atlases_surfaces_not_distributed/lh.Schaefer2018_800Parcels_7Networks_order.annot
D       atlases_surfaces_32k/rh.Schaefer2018_1000Parcels_17Networks_order.annot
        > moved to atlases_surfaces_not_distributed/rh.Schaefer2018_1000Parcels_17Networks_order.annot
D       atlases_surfaces_32k/rh.Schaefer2018_1000Parcels_7Networks_order.annot
        > moved to atlases_surfaces_not_distributed/rh.Schaefer2018_1000Parcels_7Networks_order.annot
D       atlases_surfaces_32k/rh.Schaefer2018_100Parcels_7Networks_order.annot
        > moved to atlases_surfaces_not_distributed/rh.Schaefer2018_100Parcels_7Networks_order.annot
D       atlases_surfaces_32k/rh.Schaefer2018_200Parcels_7Networks_order.annot
        > moved to atlases_surfaces_not_distributed/rh.Schaefer2018_200Parcels_7Networks_order.annot
D       atlases_surfaces_32k/rh.Schaefer2018_400Parcels_7Networks_order.annot
        > moved to atlases_surfaces_not_distributed/rh.Schaefer2018_400Parcels_7Networks_order.annot
D       atlases_surfaces_32k/rh.Schaefer2018_600Parcels_7Networks_order.annot
        > moved to atlases_surfaces_not_distributed/rh.Schaefer2018_600Parcels_7Networks_order.annot
D       atlases_surfaces_32k/rh.Schaefer2018_800Parcels_17Networks_order.annot
        > moved to atlases_surfaces_not_distributed/rh.Schaefer2018_800Parcels_17Networks_order.annot
D       atlases_surfaces_32k/rh.Schaefer2018_800Parcels_7Networks_order.annot
        > moved to atlases_surfaces_not_distributed/rh.Schaefer2018_800Parcels_7Networks_order.annot
A  +    atlases_surfaces_not_distributed/lh.Schaefer2018_1000Parcels_17Networks_order.annot
        > moved from atlases_surfaces_32k/lh.Schaefer2018_1000Parcels_17Networks_order.annot
A  +    atlases_surfaces_not_distributed/lh.Schaefer2018_1000Parcels_7Networks_order.annot
        > moved from atlases_surfaces_32k/lh.Schaefer2018_1000Parcels_7Networks_order.annot
A  +    atlases_surfaces_not_distributed/lh.Schaefer2018_100Parcels_7Networks_order.annot
        > moved from atlases_surfaces_32k/lh.Schaefer2018_100Parcels_7Networks_order.annot
A  +    atlases_surfaces_not_distributed/lh.Schaefer2018_200Parcels_7Networks_order.annot
        > moved from atlases_surfaces_32k/lh.Schaefer2018_200Parcels_7Networks_order.annot
A  +    atlases_surfaces_not_distributed/lh.Schaefer2018_400Parcels_7Networks_order.annot
        > moved from atlases_surfaces_32k/lh.Schaefer2018_400Parcels_7Networks_order.annot
A  +    atlases_surfaces_not_distributed/lh.Schaefer2018_600Parcels_7Networks_order.annot
        > moved from atlases_surfaces_32k/lh.Schaefer2018_600Parcels_7Networks_order.annot
A  +    atlases_surfaces_not_distributed/lh.Schaefer2018_800Parcels_17Networks_order.annot
        > moved from atlases_surfaces_32k/lh.Schaefer2018_800Parcels_17Networks_order.annot
A  +    atlases_surfaces_not_distributed/lh.Schaefer2018_800Parcels_7Networks_order.annot
        > moved from atlases_surfaces_32k/lh.Schaefer2018_800Parcels_7Networks_order.annot
A  +    atlases_surfaces_not_distributed/rh.Schaefer2018_1000Parcels_17Networks_order.annot
        > moved from atlases_surfaces_32k/rh.Schaefer2018_1000Parcels_17Networks_order.annot
A  +    atlases_surfaces_not_distributed/rh.Schaefer2018_1000Parcels_7Networks_order.annot
        > moved from atlases_surfaces_32k/rh.Schaefer2018_1000Parcels_7Networks_order.annot
A  +    atlases_surfaces_not_distributed/rh.Schaefer2018_100Parcels_7Networks_order.annot
        > moved from atlases_surfaces_32k/rh.Schaefer2018_100Parcels_7Networks_order.annot
A  +    atlases_surfaces_not_distributed/rh.Schaefer2018_200Parcels_7Networks_order.annot
        > moved from atlases_surfaces_32k/rh.Schaefer2018_200Parcels_7Networks_order.annot
A  +    atlases_surfaces_not_distributed/rh.Schaefer2018_400Parcels_7Networks_order.annot
        > moved from atlases_surfaces_32k/rh.Schaefer2018_400Parcels_7Networks_order.annot
A  +    atlases_surfaces_not_distributed/rh.Schaefer2018_600Parcels_7Networks_order.annot
        > moved from atlases_surfaces_32k/rh.Schaefer2018_600Parcels_7Networks_order.annot
A  +    atlases_surfaces_not_distributed/rh.Schaefer2018_800Parcels_17Networks_order.annot
        > moved from atlases_surfaces_32k/rh.Schaefer2018_800Parcels_17Networks_order.annot
A  +    atlases_surfaces_not_distributed/rh.Schaefer2018_800Parcels_7Networks_order.annot
        > moved from atlases_surfaces_32k/rh.Schaefer2018_800Parcels_7Networks_order.annot
M       cat_conf_ROI.m
M       cat_defaults.m
M       cat_vol_defs.m
M       html/cat.html
M       standalone/cat_standalone_segment.txt
A       templates_volumes/Schaefer2018_100Parcels_17Networks_order.csv
A       templates_volumes/Schaefer2018_100Parcels_17Networks_order.nii
A       templates_volumes/Schaefer2018_200Parcels_17Networks_order.csv
A       templates_volumes/Schaefer2018_200Parcels_17Networks_order.nii
A       templates_volumes/Schaefer2018_400Parcels_17Networks_order.csv
A       templates_volumes/Schaefer2018_400Parcels_17Networks_order.nii
A       templates_volumes/Schaefer2018_600Parcels_17Networks_order.csv
A       templates_volumes/Schaefer2018_600Parcels_17Networks_order.nii
A       templates_volumes/aal3.csv
A       templates_volumes/aal3.nii
A       templates_volumes/aal3.txt

(1) Added: Added Schaefer volume atlases.
(2) Changed. For categorical interpolation in "Apply deformations" the data
    type is automatically chosen according to maximum value in the label image.
(3) Changed: Removed Schaefer atlases with > 600 parcellations.
(4) Changed: Updated atlas information in all tools.

------------------------------------------------------------------------
r1594 | gaser | 2020-03-30 16:55:33 +0200 (Mon, 30 Mar 2020) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m

Fixed: Corrected dependency names in cat_conf_tools.m that caused errors in
longitudinal batch mode.


------------------------------------------------------------------------
r1593 | gaser | 2020-03-30 16:40:48 +0200 (Mon, 30 Mar 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_run.m
 M      cat_surf_load.m

Changed: Editor in cat_run.m will not open anymore in headless mode.

------------------------------------------------------------------------
r1592 | gaser | 2020-03-24 00:10:39 +0100 (Tue, 24 Mar 2020) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m

Fixed: Corrected help string in cat_conf_tools.m that caused errors.

------------------------------------------------------------------------
r1591 | gaser | 2020-03-23 23:20:09 +0100 (Mon, 23 Mar 2020) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_tools.m
M       cat_vol_groupwise_ls.m
M       html/cat.html
M       html/cat_versions.html
 M      templates_surfaces/mesh.central.Template_T1_IXI555_MNI152_GS.gii
 M      templates_surfaces_32k/mesh.central.Template_T1_IXI555_MNI152_GS.gii
M       templates_volumes/cobra.nii

(1) Changed: Average image in cat_vol_groupwise_ls.m is using median for
    rigid and mean for non-linear registration.
(2) Changed: Decreased FOV for Cobra atlas.
(3) Changed: Updated online help and manual.

------------------------------------------------------------------------
r1590 | dahnke | 2020-03-23 08:38:58 +0100 (Mon, 23 Mar 2020) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_spm_results_ui.m
A       cat_surf_load.m
M       cat_surf_parameters.m
M       cat_surf_rename.m
M       cat_surf_render.m

(1)  Changed:   Added colormap change for satellite result figure.
(2)  Fixed:     Corrected output of cat_surf_rename in case of missing parameters.
(3)  New:       Added new function cat_surf_load to combine different surface data
                files into one single mesh structure used in the cat_surf_render
                function called by cat_surf_spm_results_ui.
(4)  New:       Added surface atlas description in the datatip function in
                cat_surf_render if the results flag is active.
(5)  Fixed:     Corrected some bugs in cat_surf_render to show the colorbar in
                cat_surf_spm_results_ui.


------------------------------------------------------------------------
r1589 | dahnke | 2020-03-19 15:41:22 +0100 (Thu, 19 Mar 2020) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_main_roi.m
M       cat_stat_spm_results_ui.m

(1)  Fixed:     Corrected further bugs in cat_stat_spm_results_ui.
(2)  Fixed:     Corrected further mapping errors in cat_main_roi.


------------------------------------------------------------------------
r1588 | gaser | 2020-03-19 10:31:26 +0100 (Thu, 19 Mar 2020) | 50 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_defaults.m
M       cat_main_reportfig.m
MM      cat_run1585/cat_conf_ROI1585.m
MM      cat_run1585/cat_conf_extopts1585.m
MM      cat_run1585/cat_conf_long1585.m
MM      cat_run1585/cat_conf_opts1585.m
MM      cat_run1585/cat_defaults1585.m
MM      cat_run1585/cat_get_defaults1585.m
MM      cat_run1585/cat_main1585.m
MM      cat_run1585/cat_main_APRG1585.m
MM      cat_run1585/cat_main_LAS1585.m
MM      cat_run1585/cat_main_amap1585.m
MM      cat_run1585/cat_main_kamap1585.m
MM      cat_run1585/cat_main_registration1585.m
MM      cat_run1585/cat_main_updateSPM1585.m
MM      cat_run1585/cat_main_updateWMHs1585.m
MM      cat_run1585/cat_run1585.m
MM      cat_run1585/cat_run_job10701585.m
MM      cat_run1585/cat_run_job1585.m
MM      cat_run1585/cat_run_job_APP_SPMfinal1585.m
 M      cat_run1585/cat_run_job_APP_SPMinit1585.m
MM      cat_run1585/cat_run_job_APP_final1585.m
MM      cat_run1585/cat_run_job_APP_init10701585.m
MM      cat_run1585/cat_run_job_APP_init1585.m
MM      cat_run1585/cat_run_job_APRGs1585.m
MM      cat_run1585/cat_run_newcatch1585.m
MM      cat_run1585/cat_surf_createCS1585.m
MM      cat_run1585/cat_surf_createCS21585.m
MM      cat_run1585/cat_vol_approx1585.m
MM      cat_run1585/cat_vol_pbt1585.m
MM      cat_stat_spm_results_ui.m
M       cat_surf_render.m
M       cat_surf_results.m
 M      check_pipeline/surf/lh.pbt.IXI002-Guys-0828-T1
 M      check_pipeline/surf/lh.pbt.IXI016-Guys-0697-T1
 M      check_pipeline/surf/lh.pbt.IXI017-Guys-0698-T1
 M      check_pipeline/surf/lh.pbt.IXI019-Guys-0702-T1
 M      check_pipeline/surf/rh.pbt.IXI002-Guys-0828-T1
 M      check_pipeline/surf/rh.pbt.IXI016-Guys-0697-T1
 M      check_pipeline/surf/rh.pbt.IXI017-Guys-0698-T1
 M      check_pipeline/surf/rh.pbt.IXI019-Guys-0702-T1
M       html/cat.html
 M      templates_surfaces/cb.central.freesurfer.gii
 M      templates_surfaces/cb.sphere.freesurfer.gii

Changed: Added changes from revision 1585 again that were lost.

------------------------------------------------------------------------
r1587 | dahnke | 2020-03-18 14:04:49 +0100 (Wed, 18 Mar 2020) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_spm_results_ui.m
M       cat_surf_render.m

(1)  Fixed:     Corrected some of the bugs in cat_stat_spm_results_ui and cat_surf_render.


------------------------------------------------------------------------
r1586 | dahnke | 2020-03-18 07:37:19 +0100 (Wed, 18 Mar 2020) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_main_reportfig.m
M       cat_main_roi.m
M       cat_stat_spm.m
M       cat_stat_spm_results_ui.m
M       cat_surf_render.m
M       cat_surf_results.m
M       cat_vol_headtrimming.m
M       templates_surfaces_32k/mesh.central.Template_T1_IXI555_MNI152_GS.gii

(1)  Fixed:     Corrected bugs in cat_vol_headtrimming.
(2)  Fixed:     Corrected problems in cat_main_roi for atlases with
                different image properties (resolution and boundary box).


------------------------------------------------------------------------
r1585 | gaser | 2020-03-17 22:31:57 +0100 (Tue, 17 Mar 2020) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_main_reportfig.m
M       cat_stat_spm.m
M       cat_surf_render.m
M       cat_surf_results.m
A       templates_surfaces/mesh.central.Template_T1_IXI555_MNI152_GS.gii
A       templates_surfaces_32k/mesh.central.Template_T1_IXI555_MNI152_GS.gii

(1) Added: Meshes for Shooting template surface.
(2) Changed: Default surface for cat_stat_spm.m back to FSAverage.
(3) Fixed: Typos.

------------------------------------------------------------------------
r1584 | dahnke | 2020-03-16 11:19:58 +0100 (Mon, 16 Mar 2020) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_main_reportfig.m
M       cat_run1173/cat_defaults1173.m
M       cat_run1173plus/cat_defaults1173plus.m
M       cat_run1445/cat_defaults1445.m
M       cat_run1585/cat_defaults1585.m
M       cat_stat_spm.m
A       cat_stat_spm_results_ui.m
M       cat_surf_render.m
M       cat_surf_render2.m
M       internal/cat_admin_create_estwrite_version.m

(1)  Fixed:     Added openGL error to prevent zombie server processes.
(2)  New:       Added cat_stat_spm_results_ui for surface statistic.
                Needs integration in CAT GUI.


------------------------------------------------------------------------
r1583 | dahnke | 2020-03-12 20:26:36 +0100 (Thu, 12 Mar 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_main_roi.m
M       cat_run.m

(1)  Fixed:     Corrected bug in ROI evaluation.

------------------------------------------------------------------------
r1582 | gaser | 2020-03-11 17:55:11 +0100 (Wed, 11 Mar 2020) | 41 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_amap.mexmaci64
M       cat_conf_stools.m
M       cat_io_report.m
M       cat_main_roi.m
M       cat_sanlm.mexmaci64
M       cat_simple.m
M       cat_vol_median3.mexmaci64
M       cat_vol_median3c.mexmaci64
M       cat_vol_qa.m
M       check_pipeline/batch_surface_pipeline.m
A       check_pipeline/surf/lh.pbt.IXI002-Guys-0828-T1
A       check_pipeline/surf/lh.pbt.IXI016-Guys-0697-T1
A       check_pipeline/surf/lh.pbt.IXI017-Guys-0698-T1
A       check_pipeline/surf/lh.pbt.IXI019-Guys-0702-T1
D       check_pipeline/surf/lh.thickness.IXI002-Guys-0828-T1
D       check_pipeline/surf/lh.thickness.IXI016-Guys-0697-T1
D       check_pipeline/surf/lh.thickness.IXI017-Guys-0698-T1
D       check_pipeline/surf/lh.thickness.IXI019-Guys-0702-T1
A       check_pipeline/surf/rh.pbt.IXI002-Guys-0828-T1
A       check_pipeline/surf/rh.pbt.IXI016-Guys-0697-T1
A       check_pipeline/surf/rh.pbt.IXI017-Guys-0698-T1
A       check_pipeline/surf/rh.pbt.IXI019-Guys-0702-T1
D       check_pipeline/surf/rh.thickness.IXI002-Guys-0828-T1
D       check_pipeline/surf/rh.thickness.IXI016-Guys-0697-T1
D       check_pipeline/surf/rh.thickness.IXI017-Guys-0698-T1
D       check_pipeline/surf/rh.thickness.IXI019-Guys-0702-T1
M       html/cat.html
M       templates_volumes/cobra.csv

(1) Fixed: Removed some inconsistencies in cobra.csv
(2) Fixed: Modified and extended batch_surface_pipeline.m to consider new
    dependencies.
(3) Fixed: Check for OS-name was not correct.
(4) Fixed: Typo for release number in cat_simple.m
(5) Fixed: Removed some smaller bugs in cat_main_roi.m
(6) Fixed: Prepared Octave compatibility in cat12.m.

------------------------------------------------------------------------
r1581 | dahnke | 2020-03-11 11:20:09 +0100 (Wed, 11 Mar 2020) | 60 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_conf_output.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_io_volctype.m
M       cat_main.m
A       cat_run1585
A       cat_run1585/cat_conf_ROI1585.m
A       cat_run1585/cat_conf_extopts1585.m
A       cat_run1585/cat_conf_long1585.m
A       cat_run1585/cat_conf_opts1585.m
A       cat_run1585/cat_defaults1585.m
A       cat_run1585/cat_get_defaults1585.m
A       cat_run1585/cat_main1585.m
A       cat_run1585/cat_main_APRG1585.m
A       cat_run1585/cat_main_LAS1585.m
A       cat_run1585/cat_main_amap1585.m
A       cat_run1585/cat_main_kamap1585.m
A       cat_run1585/cat_main_registration1585.m
A       cat_run1585/cat_main_updateSPM1585.m
A       cat_run1585/cat_main_updateWMHs1585.m
A       cat_run1585/cat_run1585.m
A       cat_run1585/cat_run_job10701585.m
A       cat_run1585/cat_run_job1585.m
A       cat_run1585/cat_run_job_APP_SPMfinal1585.m
A       cat_run1585/cat_run_job_APP_SPMinit1585.m
A       cat_run1585/cat_run_job_APP_final1585.m
A       cat_run1585/cat_run_job_APP_init10701585.m
A       cat_run1585/cat_run_job_APP_init1585.m
A       cat_run1585/cat_run_job_APRGs1585.m
A       cat_run1585/cat_run_newcatch1585.m
A       cat_run1585/cat_surf_createCS1585.m
A       cat_run1585/cat_surf_createCS21585.m
A       cat_run1585/cat_vol_approx1585.m
A       cat_run1585/cat_vol_pbt1585.m
M       cat_simple.m
M       cat_surf_parameters.m
M       cat_surf_resamp.m
M       cat_vol_maskimage.m
M       internal/cat_admin_create_estwrite_version.m
M       tbx_cfg_cat.m
A       templates_surfaces/cb.central.freesurfer.gii
A       templates_surfaces/cb.sphere.freesurfer.gii

(1)  Fixed:     Corrected DEPs in cat_io_volctype and cat_vol_maskimage.
(2)  Fixed:     Corrected DEPs in cat_surf_resamp and cat_conf_stools.
(2)  Fixed:     Corrected bug in cat_simple.
(3)  Fixed:     Corrected bugs in cat_admin_create_estwrite_version.
(4)  Fixed:     Corrected bug in cat_main in relation to SPMpp batch.
(5)  Fixed:     Corrected bug for gyrification output in cat_surf_parameters.

(6)  New:       Added stable preprocessing batch 1585 with new directory
                and changes in tbx_cfg_cat, cat_conf_output, cat_simple,
                and cat12.
(7)  New:       Added cb surfaces.
{U+2248}


------------------------------------------------------------------------
r1580 | gaser | 2020-03-10 15:08:43 +0100 (Tue, 10 Mar 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_io_report.m
M       cat_vol_qa.m

Fixed: Estimation of operation system was not correct.

------------------------------------------------------------------------
r1579 | gaser | 2020-03-10 14:51:42 +0100 (Tue, 10 Mar 2020) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat12.m
MM      cat_io_lazy.m
M       cat_surf_results.m
M       html/cat.html

(1) Fixed: Removed inconsistencies in cat_surf_results.
(2) Fixed: Variable cat_version was not set in cat12.m
(3) Changed: Added checklist to Makefile


------------------------------------------------------------------------
r1578 | gaser | 2020-03-10 10:19:19 +0100 (Tue, 10 Mar 2020) | 22 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
MM      cat_io_rerun.m
M       cat_surf_results.m
 M      cat_surf_scaling.m
M       cat_version.m
M       cat_vol_slice_overlay.m
M       html/cat.html
MM      spm_diffeo_old.c
 M      spm_diffeo_old.mexa64
 M      spm_diffeo_old.mexmaci64
 M      spm_diffeo_old.mexw64

(1) Changed: Lots of changes in cat_surf_results.
(2) Changed: Made changes back in cat_version.m because Contents.txt should be
    found first for deployed versions.
(3) Changed: Timer call of update-check and server request in cat12.m to
    prevent delayed GUI responses.


------------------------------------------------------------------------
r1577 | dahnke | 2020-03-09 18:36:03 +0100 (Mon, 09 Mar 2020) | 51 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_catsimple.m
M       cat_conf_output.m
M       cat_conf_stools.m
M       cat_conf_tools.m
A       cat_io_lazy.m
M       cat_io_report.m
M       cat_main.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_main_roi.m
M       cat_main_write.m
M       cat_run1173/cat_main1173.m
M       cat_run1173/cat_tst_qa1173.m
M       cat_run1173plus/cat_main1173plus.m
M       cat_run1445/cat_conf_ROI1445.m
M       cat_run1445/cat_main1445.m
M       cat_run1445/cat_main_LAS1445.m
M       cat_run1445/cat_main_gcut1445.m
M       cat_run1445/cat_main_registration1445.m
M       cat_run1445/cat_run1445.m
M       cat_run1445/cat_run_job1445.m
M       cat_run1445/cat_run_newcatch1445.m
M       cat_run_job.m
M       cat_stat_check_SPM.m
M       cat_stat_check_cov.m
M       cat_stat_spm2x.m
M       cat_surf_fun.m
M       cat_surf_render2.m
M       cat_surf_results.m
M       cat_version.m
M       cat_vol_qa.m
M       cat_vol_sanlm.m
M       tbx_cfg_cat.m

(1)  Changed:   Added OS system and CAT segmentation version to CAT reports
                in cat_main_reportstr, cat_vol_qa, cat_io_report.
(2)  Fixed:     Corrected function calls in pipeline 1445 and 1173 in
                cat_conf_output
(3)  New:       Added contrast manager for surface in cat_conf_stools.
(4)  Updated:   Removed colorbar settings from cat_surf_render GUI in cat_conf_stools.
(5)  New:       Added functions to save and close figure in cat_stat_check_cov and
                cat_stat_check_SPM and control fields on the developer GUI.
(6)  Fixed:     Corrected bugs in CAT preprocessing with SPM input segmentation
                in cat_main, cat_main_reportfig, cat_main_roi, cat_run_job, and cat_main_write.
(7)  Fixed:     Corrected incorrect dependencies in cat_vol_sanlm
(8)  Changed:   Added output of empty files in cat_stat_spm2x to support dependencies.
(9)  Fixed:     Corrected definition in cat_version (first Content.m then Content.txt)


------------------------------------------------------------------------
r1576 | gaser | 2020-03-04 14:38:09 +0100 (Wed, 04 Mar 2020) | 20 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_conf_stools.m
M       cat_conf_stoolsexp.m
M       cat_main.m
M       cat_surf_parameters.m
M       cat_surf_results.m
M       check_pipeline.sh
M       html/cat.html
M       html/cat_methods_RBM.html
M       html/cat_starting.html
M       html/cat_versions.html

(1) Changed: Lots of changes in cat_surf_results.
(2) Changed: Updated online help.
(3) Fixed: Surface ROI estimation during preprocessing selected too many atlases.


------------------------------------------------------------------------
r1575 | dahnke | 2020-03-03 12:49:34 +0100 (Tue, 03 Mar 2020) | 40 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_io_FreeSurfer.m
A       cat_io_rerun.m
M       cat_main_gintnorm.m
M       cat_parallelize.m
M       cat_run.m
M       cat_spm_preproc8.m
M       cat_stat_spm.m
M       cat_surf_fun.m
M       cat_surf_parameters.m
M       cat_surf_render2.m
M       cat_surf_resamp.m
M       cat_surf_results.m
A       cat_surf_scaling.m

(1)  Changed:   Updated GUI and management of additional surface measures in cat_surf_param
                and cat_conf_stools. Removed other thickness measures from the expert GUI
                because Tfs is now part of the default processing. Prepared scaled/normalized
                surface measures in the development mode that are currently under test.
(2)  Changed:   Update command line progress output in cat_surf_resamp and cat_surf_parameters.
(3)  New:       Added batch support for surface statistic in cat_stat_spm and cat_conf_stools.
(4)  Fixed:     Corrected bug in cat_io_FreeSurfer to map Freesurfer surface data to gifti ('fs2gii').
(5)  Fixed:     Corrected rare bug in cat_main_gintnorm.
(6)  Fixed:     Reset bias correction changes in cat_spm_preproc8 that caused multiple errors.
                Reset SPM accuracy defaults in cat_defaults and cat_run.
(7)  Fixed:     Corrected errors in area estimation/mapping in cat_resamp. Worked on improving
                area mapping from faces to vertices in cat_surf_fun:cat_surf_area but did not
                finish it yet.
(8)  New:       Added cat_io_rerun function that estimates if a file needs to be reprocessed
                when it input-file has changes (used e.g. in cat_surf_parameters).
(9)  New:       Added cat_surf_scaling to estimate a global scaling factors to improve
                scaling invariance of different brain folding measures in cat_surf_parameters.
(10) Fixed:     Corrected command line progress output in cat_parallelize.
(11) Fixed:     Corrected display bugs in cat_surf_render2.
(12) Fixed:     Corrected bug in surface based GM volume estimation but it still needs a
                final evaluation.

------------------------------------------------------------------------
r1574 | gaser | 2020-03-03 00:55:15 +0100 (Tue, 03 Mar 2020) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_io_checkdepfiles.m
M       cat_main_registration2.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_results.m
M       cat_vol_slice_overlay_ui.m
M       standalone/cat_standalone_segment.txt

(1) Fixed: Updated new templyte_volumes folder in remaining functions,
(2) Changed: Added suppression of annoying subscripting warning.
(3) Fixed: Added warning that spm12 update is necessary for new contour
    overlay function in cat_surf_results.m.

------------------------------------------------------------------------
r1573 | gaser | 2020-03-02 22:30:34 +0100 (Mon, 02 Mar 2020) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
A       spm_diffeo_old.c
A       spm_diffeo_old.mexa64
A       spm_diffeo_old.mexmaci64
A       spm_diffeo_old.mexw64

Added: spm_diffeo.mexmaci from previous SPM12 release that were more stable for
non-linear longitudinal registration.

------------------------------------------------------------------------
r1572 | gaser | 2020-03-02 12:50:29 +0100 (Mon, 02 Mar 2020) | 19 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_surf_info.m
M       cat_surf_results.m
M       check_pipeline.sh
M       html/cat.html

(1) Changed: option to save files in a defined folder in check_pipeline.sh.
(2) Changed: Added functionality to cat_surf_results to map results from 3D
    volume data to the surface. Volumes are mapped using a absmax mapping
    function inside the cortical band of the Dartel/Shooting surface template.
(3) Fixed: Solved smaller inconsistencies in cat_surf_results if you select
    a different results file in the GUI.
(4) Changed: Updated cat_surf_info to deal with volume files which allows
    to use this function also for volumes in cat_surf_results.


------------------------------------------------------------------------
r1571 | gaser | 2020-02-27 15:51:11 +0100 (Thu, 27 Feb 2020) | 70 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Contents_info.txt
M       Makefile
A  +    aal.csv
        > moved from templates_volumes/aal.csv
A  +    aal.nii
        > moved from templates_volumes/aal.nii
A  +    aal.txt
        > moved from templates_volumes/aal.txt
M       batches/cat12batch_RBM_and_SBM_for_SPM.m
M       batches/cattest/cat12_101_MAIN_segment.m
M       batches/cattest/cat12_104_MAIN_segment_SPM.m
M       batches/cattest/cat12_105_MAIN_segment_1173plus.m
M       batches/cattest/cat12_106_MAIN_segment_1173.m
M       batches/cattest/cat12_201_VBM_deformation.m
M       cat_conf_ROI.m
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_install_atlases.m
M       cat_main_registration.m
M       cat_run1173/cat_conf_ROI1173.m
M       cat_run1173/cat_defaults1173.m
M       cat_run1173/cat_main_registration1173.m
M       cat_run1173plus/cat_defaults1173plus.m
M       cat_run1445/cat_conf_ROI1445.m
M       cat_run1445/cat_defaults1445.m
M       cat_run1445/cat_main_registration1445.m
M       cat_simple.m
M       cat_stat_spm2x.m
M       cat_surf_display.m
M       cat_surf_render2.m
M       cat_surf_surf2roi.m
M       cat_tst_cattest.m
M       cat_update.m
M       cat_vol_atlas.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_rgb_ui.m
M       check_pipeline/batch_volume_pipeline.m
M       html/cat.html
M       html/cat.txt
M       html/cat_licences.html
M       html/cat_methods_RBM.html
M       html/cat_references.html
M       html/cat_versions.html
M       internal/cat_example_surfsmooth.m
M       internal/cat_vol_atlas.m
M       internal/cat_vol_optimizeTemplate.m
M       standalone/cat_standalone_simple.txt
D       templates_1.50mm
        > moved to templates_volumes
A  +    templates_volumes
        > moved from templates_1.50mm
D  +    templates_volumes/aal.csv
        > moved to aal.csv
D  +    templates_volumes/aal.nii
        > moved to aal.nii
D  +    templates_volumes/aal.txt
        > moved to aal.txt

(1) Changed: Added AAL3 atlas and removed old AAL atlas.
(2) Changed: Renamed template folder for volumes to "templates_volumes" and
    changed all functions with references to this folder.
(3) Changed: Updated version information.
(4) Changed: Atlases that are installed in spm12/atlas are now named
    cat12_atlasname.
(5) Changed: Added Matlab links to online help for references.
(6) Fixed: Interactive call to cat_stat_spm2x was missing some parameters.

------------------------------------------------------------------------
r1570 | gaser | 2020-02-24 15:08:56 +0100 (Mon, 24 Feb 2020) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_groupwise_ls.m

Changed all calls in cat_vol_groupwise_ls.m to old spm_diffeo function because
for many data the Hessian matrix could not be estimated.


------------------------------------------------------------------------
r1569 | gaser | 2020-02-24 14:24:47 +0100 (Mon, 24 Feb 2020) | 17 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_main_gintnorm.m
M       cat_run.m
M       cat_vol_groupwise_ls.m
M       html/cat.html
 M      html/cat_licences.html
 M      html/cat_references.html
M       html/cat_statistics.html

(1) Changed: Disabled send of piwik information about number of processed files.
(2) Changed: Added call to old spm_diffeo function for fmg if the new functions
    ends up in NaNs in cat_vol_groupwise_ls.m.
(3) Changed: Updated parameters for MT contrasts with strong background noise.

------------------------------------------------------------------------
r1568 | gaser | 2020-02-14 15:37:03 +0100 (Fri, 14 Feb 2020) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_ROI.m
M       cat_run.m
M       html/cat.html

Fixed: Writing of surface ROIs were not recognized in cat_run.m for default
user mode.

------------------------------------------------------------------------
r1567 | gaser | 2020-02-14 13:49:49 +0100 (Fri, 14 Feb 2020) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       html/cat.html
M       html/cat.txt
M       html/cat_acknowledgement.html
A       html/cat_licences.html
A       html/cat_references.html
D       use_of_external_software.txt

(1) Changed: Added license information about used software and atlases.
(2) Changed: Added site with references for citation.


------------------------------------------------------------------------
r1566 | gaser | 2020-02-13 11:25:08 +0100 (Thu, 13 Feb 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_vol2surf.m

Fixed: If only one step is defined for volume mapping force use of "max" as
sampling function.

------------------------------------------------------------------------
r1565 | gaser | 2020-02-13 10:58:08 +0100 (Thu, 13 Feb 2020) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_ROI.m
M       cat_conf_stools.m
M       cat_defaults.m
MM      cat_io_send_to_server.m
M       cat_run.m
M       templates_1.50mm/lpba40.txt
M       use_of_external_software.txt

(1) Changed: Updated license information for atlases and added printing of
    licene information for LPBA40 and Hammers atlas.
(2) Changed: Updated defaults for atlases.
(3) Changed: Recompiled CAT-binaries because of error in CAT_3dVol2Surf for
    equi-volume mapping.

------------------------------------------------------------------------
r1564 | gaser | 2020-02-11 17:10:56 +0100 (Tue, 11 Feb 2020) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_ROI.m
M       html/cat.html
 M      templates_surfaces/mesh.inflated.freesurfer.gii
 M      templates_surfaces_32k/mesh.inflated.freesurfer.gii

Fixed: Typos...

------------------------------------------------------------------------
r1563 | gaser | 2020-02-11 17:00:46 +0100 (Tue, 11 Feb 2020) | 23 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat12.m
M       cat_install_tfce.m
A       cat_io_send_to_server.m
M       cat_main_reportfig.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_newcatch.m
M       cat_stat_confplot_spm.m
M       cat_update.m
M       html/cat.html
M       html/cat_statistics.html

1. Changed: Updated ip-address for piwik server and cat12-files.
2. Changed: Added new function to send information to piwik-server.
3. Changed: Now, only the number of processed files are sent to piwik server.
4. Fixed: Plot for parameter estimates in cat_stat_confplot_spm.m was falsly
   limited to two effects.


------------------------------------------------------------------------
r1562 | dahnke | 2020-02-11 14:53:30 +0100 (Tue, 11 Feb 2020) | 37 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_ROI.m
M       cat_conf_output.m
M       cat_defaults.m
M       cat_get_defaults.m
M       cat_main.m
M       cat_main_roi.m
M       cat_run.m
M       cat_stat_check_cov2.m
M       cat_surf_render.m
M       cat_surf_render2.m
M       cat_surf_resamp.m
M       cat_surf_surf2roi.m
M       html/cat_methods_RBM.html
M       tbx_cfg_cat.m
A       templates_surfaces/mesh.inflated.freesurfer.gii
A       templates_surfaces_32k/mesh.inflated.freesurfer.gii

(1) New:      Added OS to CAT report.
(2) Changed:  Updated camlight setting in cat_surf_render(2) to avoid
              shadows by using frontal light.
(3) Fixed:    Corrected bug in cat_surf_render input in developer mode.
(4) Fixed:    Corrected bug in cat_stat_checkcov2.
(5) Fixed:    Corrected bug in cat_surf_resamp that depends on the
              input structures of different user levels.
(6) Changed:  Updated cat_get_defaults for cell updates.
(7) Changed:  Updated cat_main_roi for WMH output in case of WMHC==3.
              Added support for own atlas maps.
(8) Changed:  Added differentiation between 32k and 160k surfaces and
              basic support of own atlas maps in cat_surf_surf2roi.
(9) New:      Added menu elements to support own volume- and surface-
              based atlas maps.  Updated surface atlas definition in
              cat_defaults, tbx_cat_defaults, cat_conf_output, cat_main
              and cat_run.


------------------------------------------------------------------------
r1561 | gaser | 2020-02-04 16:49:34 +0100 (Tue, 04 Feb 2020) | 23 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main_LAS.m
M       cat_main_registration.m
M       cat_main_updateSPM.m
M       cat_ornlm.m
M       cat_run.m
M       cat_run_job_APP_SPMinit.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_vol_atlas.m
M       cat_vol_correct_slice_scaling.m
M       cat_vol_laplace3.c
M       cat_vol_laplace3.m
M       cat_vol_laplace3R.c
M       cat_vol_laplace3R.m
M       html/cat.html

1. Changed: Added side-name to pp-file in cat_surf_createCS*.m.
2. Fixed: Corrected typos...


------------------------------------------------------------------------
r1560 | dahnke | 2020-01-30 15:38:24 +0100 (Thu, 30 Jan 2020) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_run.m
M       cat_run_job.m
M       cat_surf_surf2roi.m

(1) Fixed:    Updated SPM parameters (opt.samp) that cause problems after
              the last SPM update (R7771). Updated also the definition of
              the opt.accstr parameter in cat_run to use 2 mm as default.
(2) Changed:  Modified XML structure of surface ROIs in cat_surf_surf2roi.


------------------------------------------------------------------------
r1559 | gaser | 2020-01-29 13:38:39 +0100 (Wed, 29 Jan 2020) | 21 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_tools.m
M       cat_main.m
M       cat_run_job.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_vol_defs.m
M       check_pipeline.sh
M       check_pipeline_ROIs.m
M       compile.m
M       html/cat.html

1. Changed: Updated size-parameter for topology correction.
2. Changed: Added categorical interpolation to deformation tools.
3. Fixed: Changed keywords to search for check_pipeline.sh.
4. Changed: Added check for send_info-flag to urlread-calls.


------------------------------------------------------------------------
r1558 | dahnke | 2020-01-29 12:28:17 +0100 (Wed, 29 Jan 2020) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_io_writenii.m
M       development/Template_0_IXI555_MNI152_GS1mm.nii

(1)  Fixed:    Corrected bug in writing single/float32 images in cat_main_write.


------------------------------------------------------------------------
r1557 | dahnke | 2020-01-29 10:34:03 +0100 (Wed, 29 Jan 2020) | 27 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_main_write.m
M       cat_run1173/cat_defaults1173.m
M       cat_run1445/cat_conf_extopts1445.m
M       cat_run1445/cat_conf_opts1445.m
M       cat_run1445/cat_defaults1445.m
M       cat_run1445/cat_get_defaults1445.m
M       cat_stat_check_cov.m
M       cat_stat_check_cov2.m
M       cat_surf_fun.m
M       cat_surf_gyrification.m
M       cat_surf_info.m
M       compile.m

(1)  Changed:  Updated changes due to cat_vol_pbt(2).c in compile function.
(2)  Fixed:    Corrected error using subversion1445 in cat_defaults1445,
               cat_get_defaults1445, cat_conf_opts1445, cat_conf_extopts1445,
               and cat
(3)  Fixed:    Corrected setting of global cat, cat1173, and cat1445 variables
               in cat_defaults, cat_defaults1173, and cat_defaults1445.
(4)  Fixed:    Switch from uint16 to single output for normalized data to avoid
               further processing problems. Thanks to Martin Gell for pointing
               out this problem.


------------------------------------------------------------------------
r1556 | gaser | 2020-01-27 17:05:27 +0100 (Mon, 27 Jan 2020) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_cat.m
M       check_pipeline.sh
M       html/cat.html
 M      use_of_external_software.txt

1. Changed: Extended check_pipline_ROIs.m for use of thickness data.
2. Changed: Added flags to cat_batch_cat.m to prevent wrnings for batch mode.


------------------------------------------------------------------------
r1555 | gaser | 2020-01-25 00:47:44 +0100 (Sat, 25 Jan 2020) | 46 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_amap.mexa64
M       cat_amap.mexw64
M       cat_ornlm.mexa64
M       cat_ornlm.mexw64
M       cat_sanlm.mexa64
M       cat_sanlm.mexw64
M       cat_vbdist.mexa64
M       cat_vbdist.mexw64
M       cat_vol_downcut.mexa64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.mexa64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.mexa64
M       cat_vol_genus0.mexmaci64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mexa64
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mexa64
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.mexa64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mexa64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexa64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexa64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexa64
M       cat_vol_median3c.mexw64
MM      cat_vol_pbtp.c
M       cat_vol_pbtp.mexa64
M       cat_vol_pbtp.mexw64
 M      cat_vol_pbtp2.c
 M      cat_vol_pbtp2.mexmaci64
M       cat_vol_simgrow.mexa64
M       cat_vol_simgrow.mexw64
M       html/cat.html
M       use_of_external_software.txt

1. Changed: Recompiled mex-files for all systems.
2. Changed: Made cat_vol_pbtp.c more conform to older gcc versions.


------------------------------------------------------------------------
r1554 | gaser | 2020-01-24 23:41:19 +0100 (Fri, 24 Jan 2020) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_vol_genus0.c
M       cat_vol_genus0.mexmaci64
M       genus0.c

(1) Fixed: Corrected error in genus0.c that caused deviations between
    different systems due to code that was not conform to C90.
(2) Changed: Removed 2nd loop for voxel-wise topology correction in
    cat_vol_genus0.c and cleaned code.
(3) Changed: Added threshold-parameter to intrnal cat_vol_genus0opt function
    in cat_surf_createCS2.m and cleaned code.
(4) Changed: Added cat_vol_genus0opt to cat_surf_createCS.m to only remove
    smaller topology defects initially in 3D space.

------------------------------------------------------------------------
r1553 | gaser | 2020-01-23 08:37:40 +0100 (Thu, 23 Jan 2020) | 55 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Contents_info.txt
M       cat_amap.mexa64
M       cat_amap.mexw64
M       cat_batch_cat.m
M       cat_ornlm.mexa64
M       cat_ornlm.mexw64
M       cat_sanlm.mexa64
M       cat_sanlm.mexw64
M       cat_stat_confplot_spm.m
M       cat_surf_results.m
M       cat_vbdist.mexa64
M       cat_vbdist.mexw64
M       cat_vol_downcut.mexa64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.mexa64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.mexa64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mexa64
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mexa64
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.mexa64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mexa64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexa64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexa64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexa64
M       cat_vol_median3c.mexw64
M       cat_vol_pbtp.mexa64
M       cat_vol_pbtp.mexmaci64
M       cat_vol_pbtp.mexw64
M       cat_vol_simgrow.mexa64
M       cat_vol_simgrow.mexw64
M       compile.m
M       html/cat.html
M       html/cat.txt
M       templates_1.50mm/aal.txt
M       templates_1.50mm/cobra.txt
A       use_of_external_software.txt

1. Changed: Updated license information.
2. Changed: Updated compile tool to consider changed files.
3. Changed: Recompiled for all systems.
4. Changed: Updated many functions in cat_surf_results and changed plotting
   for raw data.
5. Changed: Updated cat_stat_confplot_spm.m to correctly consider covariates.
6. Changed: Added new flags to cat_batch_cat.m.

------------------------------------------------------------------------
r1552 | dahnke | 2020-01-17 11:19:24 +0100 (Fri, 17 Jan 2020) | 65 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_io_report.m
M       cat_main.m
M       cat_main_amap.m
M       cat_main_registration.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_plot_boxplot.m
M       cat_run.m
M       cat_run1173/cat_main1173.m
M       cat_run1173plus/cat_main1173plus.m
M       cat_run_job.m
M       cat_run_newcatch.m
M       cat_spm_preproc8.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m
M       cat_tst_BWPsliceartifact.m
M       cat_vol_pbt.m
M       cat_vol_pbt2.m
A       cat_vol_pbtp.c
M       cat_vol_pbtp.mexmaci64
A       cat_vol_pbtp2.c
A       cat_vol_pbtp2.mexmaci64
M       cat_vol_qa.m
M       cat_vol_sanlm.m
M       cat_vol_urqio.m
M       tbx_cfg_cat.m

(1)  Changed:  Updated GUI to control mesh resolution of cat_surf_createCS2 in
               cat_conf_extopts, supporting now also lower mesh-resolutions by
               mesh generation at lower volume resolutions.
               Updated surface parameters in cat_defaults to control mesh
               creation (reduce_mesh) and resolution (vdist) used in
               cat_surf_createCS2.
(2)  Changed:  Small updates of cat_surf_collcorr in cat_surf_fun.
(3)  Fixed:	   Corrected batch dependencies of additional surfaces and measures
               in tbx_cfg_cat and cat_run.
(4)  Fixed:    Corrections for bad inputs in cat_plot_boxplot.
(5)  Fixed:    Many corrections in cat_surf_createCS(2) to avoid different
               results if the processing order of left and right hemisphere
               is switched.
(6)  Fixed:    Added/updated seed definition in cat_vol_sanlm, cat_main_amap,
               cat_spm_preproc, cat_tst_BWPsliceartifact, and cat_vol_urquio.
(7)  Fixed:    Corrected "strfindi" error in cat_run_newcatch.
(8)  Fixed:    Avoid creation of diary file if another file is used and
               display a warning (cat_run_job).
(9)  Fixed:    Replaced cat_vol_pbtp from cpp to c, and added an improved
               version cat_vol_pbtp2.c for cat_surf_createCS2.
(10) Fixed:    Corrected bug in the layer4 evaluation in cat_surf_evalCS in
               cat_surf_fun.
(12) Fixed:    Added abs in a definition in cat_vol_qa to avoid problems
               with negative values.
(13) Fixed:    Corrected displaying of the segmentation in the error report
               in cat_io_report and cat_main.
(14) Fixed:    Deactivated seed generation warning in cat_main_registration.
(15) Fixed:    Display CS in CAT report (cat_main_reportfig) if collcorr<20
               and no developer mode is used.
(16) Fixed:    Removed SPM accuracy line from the CAT report of standard user
               in cat_main_reportstr.


------------------------------------------------------------------------
r1551 | gaser | 2020-01-13 09:33:37 +0100 (Mon, 13 Jan 2020) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_plot_boxplot.m
M       cat_stat_confplot_spm.m
M       cat_surf_results.m
M       html/cat.html

1. Changed: Added adjustement for plotting raw data to cat_stat_confplot_spm.m.
2. Changed: Updated help text for cat_plot_boxplot.m.
3. Changed: Updated adjustment for raw data in cat_surf_results and added
   boxplot for raw data.

------------------------------------------------------------------------
r1550 | gaser | 2020-01-08 15:59:58 +0100 (Wed, 08 Jan 2020) | 39 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_amap.mexa64
M       cat_amap.mexw64
M       cat_ornlm.mexa64
M       cat_ornlm.mexw64
M       cat_sanlm.mexa64
M       cat_sanlm.mexw64
M       cat_vbdist.mexa64
M       cat_vbdist.mexw64
M       cat_vol_downcut.mexa64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.mexa64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.mexa64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mexa64
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mexa64
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.mexa64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mexa64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexa64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexa64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexa64
M       cat_vol_median3c.mexw64
M       cat_vol_pbtp.mexa64
M       cat_vol_pbtp.mexw64
M       cat_vol_simgrow.mexa64
M       cat_vol_simgrow.mexw64
M       html/cat.html

(Changed: Recompiled mex-files and CAT-binaries with new optimized flags.

------------------------------------------------------------------------
r1549 | gaser | 2020-01-08 11:00:23 +0100 (Wed, 08 Jan 2020) | 31 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_amap.mexmaci64
M       cat_ornlm.mexmaci64
M       cat_run.m
M       cat_sanlm.mexmaci64
M       cat_surf_createCS.m
M       cat_surf_fun.m
M       cat_vbdist.mexmaci64
M       cat_vol_downcut.mexmaci64
M       cat_vol_eidist.mexmaci64
M       cat_vol_genus0.mexmaci64
M       cat_vol_gradient3.mexmaci64
M       cat_vol_interp3f.mexmaci64
M       cat_vol_laplace3.mexmaci64
M       cat_vol_laplace3R.mexmaci64
M       cat_vol_localstat.mexmaci64
M       cat_vol_median3.mexmaci64
M       cat_vol_median3c.mexmaci64
M       cat_vol_pbtp.mexmaci64
M       cat_vol_simgrow.mexmaci64
M       compile.m
M       html/cat.html
M       internal/cat_vol_cMRegularizarNLM3D.mexmaci64

(1) Changed: Optimized flags for compiling.
(2) Changed: Tried to get rid of annoying subscript warning for gifti function
    again.
(3) Changed: Removed layer4 from dependency list in cat_run.m.

------------------------------------------------------------------------
r1548 | gaser | 2020-01-07 14:20:08 +0100 (Tue, 07 Jan 2020) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main_reportstr.m
MM      cat_vol_pbt2.m
M       html/cat_methods_templates.html
M       html/cat_starting_cattest.html
M       html/cat_versions.html

(1) Changed: Updated help text.
(2) Changed: Updated version information.

------------------------------------------------------------------------
r1547 | gaser | 2020-01-07 10:54:52 +0100 (Tue, 07 Jan 2020) | 6 lines

Changed paths:
M       CHANGES.txt
M       html/cat_versions.html

Changed: Corrected some typos.

------------------------------------------------------------------------
r1546 | gaser | 2020-01-05 22:38:09 +0100 (Sun, 05 Jan 2020) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m
M       cat_vol_slice_overlay.m

(1) Fixed: Corrected path of output image file for cat_vol_slice_overlay.m.
(2) Changed: Disabled some widgets in cat_surf_results after start.

------------------------------------------------------------------------
r1545 | gaser | 2020-01-05 21:37:52 +0100 (Sun, 05 Jan 2020) | 6 lines

Changed paths:
M       CHANGES.txt
A       cat_vol_pbt2.m

Fixed: Again added deleted cat_vol_pbt2.m

------------------------------------------------------------------------
r1544 | gaser | 2020-01-05 21:36:13 +0100 (Sun, 05 Jan 2020) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
D       cat_vol_pbt2.m

Changed: Suppress annoying subscripts warning in combination with
spm_mesh_join.m

------------------------------------------------------------------------
r1543 | gaser | 2019-12-30 17:20:10 +0100 (Mon, 30 Dec 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m

Fixed: Removed some inconsistencies in cat_surf_results.m.

------------------------------------------------------------------------
r1542 | gaser | 2019-12-30 16:47:26 +0100 (Mon, 30 Dec 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m

Fixed: Global parameter H was removed by accident.

------------------------------------------------------------------------
r1541 | gaser | 2019-12-30 16:35:48 +0100 (Mon, 30 Dec 2019) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_confplot_spm.m
M       cat_surf_results.m

Changed: Undo renaming of global parameter H in some functions und rather
delete variable with flag -globalvar after closing.

------------------------------------------------------------------------
r1540 | gaser | 2019-12-30 15:50:59 +0100 (Mon, 30 Dec 2019) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_confplot_spm.m
M       cat_surf_results.m

(1) Changed: Renamed global parameter H in some functions to not interfere
    between these functions.
(3) Changed: Use new approach to overlay atlas borders that results in finer
    lines in cat_surf_results.m
(4) Fixed: Subject factors were only available in repeated anova designs in
    cat_stat_confplot_spm.m.

------------------------------------------------------------------------
r1539 | gaser | 2019-12-30 09:46:05 +0100 (Mon, 30 Dec 2019) | 19 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       cat_run_newcatch.m
M       cat_surf_resamp.m
M       cat_surf_results.m
M       html/cat.html
M       html/cat_starting.html

(1) Changed: Extraction of ROI-based thickness is not necessary anymore because
    this is now included in the segmentation pipeline in cat_main.m.
(2) Changed: Updated Quick Start Guide.
(3) Fixed: cat_surf_results now intercepts empty varargin field.
(4) Changed: Removed unnecessary 2nd cell structure for input data in
    cat_surf_resamp.m.
(5) Fixed: Commented out missing strfindi function and testmessage in
    cat_run_newcatch.m.

------------------------------------------------------------------------
r1538 | gaser | 2019-12-18 15:48:43 +0100 (Wed, 18 Dec 2019) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_catsimple.m
M       cat_run.m

(1) Fixed: Corrected dependencies in cat_run.m.
(2) Fixed: Corrected registration options for simple processing in expert mode.


------------------------------------------------------------------------
r1537 | gaser | 2019-12-18 11:16:23 +0100 (Wed, 18 Dec 2019) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_catsimple.m
M       cat_conf_stools.m
M       cat_simple.m
M       cat_surf_resamp.m
M       spm_cat12.m
M       standalone/cat_standalone_resample.txt
M       tbx_cfg_cat.m

(1) Changed: Added check that CAT12 is not installed with multiple instances.
(2) Changed: Corrected unnecessary data_surf cell-structure for resampling batch.


------------------------------------------------------------------------
r1536 | gaser | 2019-12-17 12:07:00 +0100 (Tue, 17 Dec 2019) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_defaults.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_results.m
MM      cat_vol_pbt2.m
M       html/cat.html

(1) Changed: Updated cat_surf_results.m for desling with two-sides meshes only.
(2) Changed: Temporary lh/rh files of ROI surface anaylsis will be deleted
    in cat_stat_analyze_ROIs.m.
(3) Changed: Disabled collision correction in cat_defaults.m that is not yet
    working properly.


------------------------------------------------------------------------
r1535 | gaser | 2019-12-13 16:40:18 +0100 (Fri, 13 Dec 2019) | 14 lines

Changed paths:
M       CHANGES.txt
MM      cat_stat_confplot_spm.m
M       cat_surf_calc.m
M       cat_surf_info.m
M       cat_surf_results.m

(1) Changed: Updated cat_surf_results.m to also allow meshes that are not
    based on fsaverage structure.
(2) Changed: Added option for fixing scaling to cat_surf_results.m.
(3) Changed: Use original mesh info in cat_surf_info.m if cdata and mesh are
    defined to also allow meshes that are not based on fsaverage.
(4) Changed: Save mesh as Base64Binary in cat_surf_calc.m

------------------------------------------------------------------------
r1534 | gaser | 2019-12-13 00:09:52 +0100 (Fri, 13 Dec 2019) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_confplot_spm.m
A       cat_vol_pbt2.m

(1) Changed: Added option to additionally plot raw data to
    cat_stat_confplot_spm.m.
(2) Fixed: Again added cat_vol_pbt2.m.

------------------------------------------------------------------------
r1533 | gaser | 2019-12-12 23:29:44 +0100 (Thu, 12 Dec 2019) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_ROI.m
M       cat_main_roi.m
M       cat_run.m
M       cat_vol_atlas.m
D       cat_vol_pbt2.m
M       templates_1.50mm/hammers.txt

(1) Changed: Updated license information of Hammers atlas and print website
    to fill out license agreement during preprocessing.
(2) Fixed: Corrected help text.

------------------------------------------------------------------------
r1532 | gaser | 2019-12-11 18:04:50 +0100 (Wed, 11 Dec 2019) | 21 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_defaults.m
M       cat_main_reportfig.m
M       cat_plot_boxplot.m
M       cat_stat_analyze_ROIs.m
A       cat_stat_confplot_spm.m
M       cat_surf_createCS2.m
M       cat_surf_results.m
M       html/cat.html

(1) Added: New tool for plotting confidence intervals and boxplots for results
    of stat. analysis.
(2) Fixed: Undefined H.merged parameter in cat_surf_results.m caused problems.
(3) Changed: Set reduce_mesh to "0" and collcorr to "20" in surface pipeline.
(4) Fixed: Boxplot with only raw data was not using "hold on" and was deleted.
(5) Fixed: Report function was not working without surfaces outputs.
(6) Fixed: ROI-analysis crashed and/or was falsified if different numbers of
    atlases were stored for a sample.

------------------------------------------------------------------------
r1531 | gaser | 2019-12-05 17:07:30 +0100 (Thu, 05 Dec 2019) | 20 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_stat_spm.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
M       cat_surf_results.m
MM      cat_vol_ROIval.m
M       cat_vol_findfiles.m
MM      cat_vol_pbt2.m

(1) Fixed: Typo that caused crash in cat_vol_findfiles.m.
(2) Fixed: Corrected unnecessary update of info filed that caused problems
    in cat_surf_results.m after switching between different results.
(3) Changed: Changed gifti-format after resampling to use external dat-files.
    This will increase processing speed and prevents that SPM.mat file for
    surfaces gets too large. This can be optionally disabled in cat_defaults.m.
(4) Changed: Reformatted cat_stat_spm.m


------------------------------------------------------------------------
r1530 | gaser | 2019-12-05 09:36:42 +0100 (Thu, 05 Dec 2019) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_main_reportstr.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m
M       cat_vol_findfiles.m

(1) Fixed: prevent use of doubled wildcards in cat_fol_findfiles.m that were
    not allowed.
(2) Changed: Disabled printout of computation time for each single step of
    collission detection in cat_surf_fun.m and reformated some code.
(3) Changed: Added some changes for compatibility for Octave.


------------------------------------------------------------------------
r1529 | dahnke | 2019-12-04 12:36:39 +0100 (Wed, 04 Dec 2019) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main.m
M       cat_main_reportfig.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m
A       cat_vol_ROIval.m

(1) Fixed:      Added alternative versions of the surface reduction.
(2) New:        Added subfunction for external call of the MATLAB reduce
                function to avoid fatal crashes
(3) Changed:    Use white/pial surface in all report figures.
(4) New:        Added orthview output for all surfaces in cat_main and
                updated cat_surf_fun>cat_surf_show_orthview.



------------------------------------------------------------------------
r1528 | gaser | 2019-12-03 12:41:21 +0100 (Tue, 03 Dec 2019) | 20 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_long.m
M       cat_conf_tools.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
D       cat_parallelize.sh
M       cat_run_job.m
M       cat_surf_createCS2.m

(1) Changed: Check wheter OpenGL is set in cat_main_reportfig.m to prevent
    crashing on headless cluster computers.
(2) Changed: Added my last changes again from previous commits that were
    overwritten.
(3) Changed: Added timeout parameter to urlread.
(4) Changed: Warping regularization for longitudinal registration is increased.
(5) Changed: Force single-processor use for shell-script calls of longitudinal
    batch.
(6) Removed: Deleted doubled cat_parallize.sh.

------------------------------------------------------------------------
r1527 | dahnke | 2019-11-29 15:01:00 +0100 (Fri, 29 Nov 2019) | 24 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_gintnorm.m
M       cat_main_roi.m
M       cat_main_write.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_newcatch.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m
M       cat_surf_resamp.m
M       cat_vol_pbt2.m
M       internal/cat_vol_nlmus.m
M       tbx_cfg_cat.m

(1) Fixed:      Corrected bugs in the new dependency definition.
(2) Changed:    Updated error message filename removal.
(3) Changed:    Updated some error messages in cat_run_job and related functions.
(4) Changed:    Updated cerebellar pipeline.
(5) Changed:    Added variable use in NLM interpolation.
(6) Docu:       Updated help in cat_surf_fun.


------------------------------------------------------------------------
r1526 | gaser | 2019-11-29 13:34:02 +0100 (Fri, 29 Nov 2019) | 25 lines

Changed paths:
M       CHANGES.txt
 M      cat_amap.mex
M       cat_main_reportfig.m
 M      cat_ornlm.mex
 M      cat_sanlm.mex
 M      cat_vbdist.mex
 M      cat_vol_downcut.mex
 M      cat_vol_eidist.mex
 M      cat_vol_genus0.mex
 M      cat_vol_gradient3.mex
 M      cat_vol_interp3f.mex
 M      cat_vol_laplace3.mex
 M      cat_vol_laplace3R.mex
 M      cat_vol_localstat.mex
 M      cat_vol_median3.mex
 M      cat_vol_median3c.mex
A       cat_vol_pbt2.m
 M      cat_vol_pbtp.mex
 M      cat_vol_simgrow.mex
 M      internal/cat_vol_cMRegularizarNLM3D.mex

(1) Fixed: Corrected settings using set in cat_main_reportfig.m.
(2) Added: cat_vol_pbt2.m was missing.

------------------------------------------------------------------------
r1525 | gaser | 2019-11-29 11:30:36 +0100 (Fri, 29 Nov 2019) | 64 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_amap.mex
M       cat_amap.mexa64
M       cat_amap.mexw64
M       cat_main_reportfig.m
M       cat_ornlm.mex
M       cat_ornlm.mexa64
M       cat_ornlm.mexw64
M       cat_run1173/cat_conf_long1173.m
M       cat_run1445/cat_conf_extopts1445.m
M       cat_run1445/cat_conf_long1445.m
M       cat_run1445/cat_conf_opts1445.m
M       cat_run1445/cat_run1445.m
M       cat_sanlm.mex
M       cat_sanlm.mexa64
M       cat_sanlm.mexw64
M       cat_vbdist.mex
M       cat_vbdist.mexa64
M       cat_vbdist.mexw64
M       cat_vol_downcut.mex
M       cat_vol_downcut.mexa64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.mex
M       cat_vol_eidist.mexa64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.mex
M       cat_vol_genus0.mexa64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mex
M       cat_vol_gradient3.mexa64
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mex
M       cat_vol_interp3f.mexa64
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.mex
M       cat_vol_laplace3.mexa64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mex
M       cat_vol_laplace3R.mexa64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mex
M       cat_vol_localstat.mexa64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mex
M       cat_vol_median3.mexa64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mex
M       cat_vol_median3c.mexa64
M       cat_vol_median3c.mexw64
M       cat_vol_pbtp.mex
M       cat_vol_pbtp.mexa64
M       cat_vol_pbtp.mexw64
M       cat_vol_simgrow.mex
M       cat_vol_simgrow.mexa64
M       cat_vol_simgrow.mexw64
M       html/cat.html
M       internal/cat_vol_cMRegularizarNLM3D.mex

(1) Fixed: Corrected typo in cat_main_reportfig.m.
(2) Changed: Recompiled mex-files.
(3) Changed: renamed function names in cat_run* folders.

------------------------------------------------------------------------
r1524 | gaser | 2019-11-28 18:00:31 +0100 (Thu, 28 Nov 2019) | 43 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_amap.mexmaci64
M       cat_io_cprintf.m
M       cat_io_csv.m
M       cat_io_matlabversion.m
M       cat_io_report.m
M       cat_main_reportfig.m
M       cat_ornlm.mexmaci64
M       cat_run_newcatch.m
M       cat_sanlm.mexmaci64
M       cat_update.m
M       cat_vbdist.mexmaci64
M       cat_vol_downcut.mexmaci64
M       cat_vol_eidist.c
M       cat_vol_eidist.mex
M       cat_vol_eidist.mexmaci64
M       cat_vol_genus0.mexmaci64
M       cat_vol_gradient3.mexmaci64
M       cat_vol_interp3f.mexmaci64
M       cat_vol_laplace3.mexmaci64
M       cat_vol_laplace3R.mexmaci64
M       cat_vol_localstat.c
M       cat_vol_localstat.mex
M       cat_vol_localstat.mexmaci64
M       cat_vol_median3.mexmaci64
M       cat_vol_median3c.mexmaci64
M       cat_vol_pbtp.cpp
MM      cat_vol_pbtp.m
M       cat_vol_pbtp.mex
M       cat_vol_pbtp.mexmaci64
MM      cat_vol_simgrow.m
M       cat_vol_simgrow.mexmaci64
M       compile.m
M       internal/cat_vol_cMRegularizarNLM3D.mexmaci64

(1) Changed: Made some Matlab code compatibe to Octave (Thanks to Guillaume
    Flandin for suggestions).
(2) Fixed: Corrected output parameters of cat_vol_pbtp.cpp.
(3) Changed: Added timeout parameter to urlread to prevent long wating times
    if server is not responding.

------------------------------------------------------------------------
r1523 | gaser | 2019-11-22 00:12:24 +0100 (Fri, 22 Nov 2019) | 83 lines

Changed paths:
M       BayesMex.c
M       CHANGES.txt
M       Contents.m
M       KmeansMex.c
M       cat12.m
M       cat_amap.c
A       cat_amap.mex
M       cat_io_findjobj.m
M       cat_main.m
M       cat_main_LAS2.m
M       cat_main_reportstr.m
M       cat_ornlm.c
A       cat_ornlm.mex
M       cat_run1173/cat_main1173.m
M       cat_run1173/cat_run_job10701173.m
M       cat_run1173/cat_run_job1173.m
M       cat_run1173/cat_surf_createCS1173.m
M       cat_run1173plus/cat_main1173plus.m
M       cat_run1173plus/cat_run_job10701173plus.m
M       cat_run1173plus/cat_run_job1173plus.m
M       cat_run1445/cat_main1445.m
M       cat_run1445/cat_run_job10701445.m
M       cat_run1445/cat_run_job1445.m
M       cat_run1445/cat_surf_createCS1445.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_sanlm.c
A       cat_sanlm.mex
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_vbdist.c
MM      cat_vbdist.m
A       cat_vbdist.mex
M       cat_vol_ROIval.c
M       cat_vol_downcut.c
MM      cat_vol_downcut.m
A       cat_vol_downcut.mex
M       cat_vol_eidist.c
MM      cat_vol_eidist.m
A       cat_vol_eidist.mex
M       cat_vol_eikonal3.c
MM      cat_vol_eikonal3.m
M       cat_vol_findfiles.m
M       cat_vol_genus0.c
MM      cat_vol_genus0.m
A       cat_vol_genus0.mex
M       cat_vol_gradient3.c
A       cat_vol_gradient3.mex
MM      cat_vol_interp3f.m
A       cat_vol_interp3f.mex
M       cat_vol_laplace3.c
MM      cat_vol_laplace3.m
A       cat_vol_laplace3.mex
M       cat_vol_laplace3R.c
MM      cat_vol_laplace3R.m
A       cat_vol_laplace3R.mex
M       cat_vol_localstat.c
MM      cat_vol_localstat.m
A       cat_vol_localstat.mex
M       cat_vol_median3.c
MM      cat_vol_median3.m
A       cat_vol_median3.mex
M       cat_vol_median3c.c
MM      cat_vol_median3c.m
A       cat_vol_median3c.mex
M       cat_vol_pbtp.cpp
A       cat_vol_pbtp.mex
M       cat_vol_pbtv.cpp
M       cat_vol_simgrow.c
A       cat_vol_simgrow.mex
M       cat_vol_slice_overlay.m
M       development/cat_surf_createCS.m
M       genus0.c
M       html/cat.html
M       internal/cat_vol_cMRegularizarNLM3D.c
A       internal/cat_vol_cMRegularizarNLM3D.mex

(1) Fixed: Made c-files compatible to Octave by removing the matrix.h header.
(2) Added: Mex-files for Octave.
(3) Changed: Made some Matlab code compatibe to Octave (Thanks to Guillaume
    Flandin for suggestions).

------------------------------------------------------------------------
r1522 | gaser | 2019-11-21 22:04:20 +0100 (Thu, 21 Nov 2019) | 25 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main_LASs.m
A  +    cat_parallelize.sh
M       cat_run.m
M       cat_stat_check_SPM.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_results.m
D       cat_vol_pbt2.m
M       cat_vol_slice_overlay.m
M       html/cat.html
M       html/cat_starting.html
MM      standalone/cat_standalone_smooth.txt

(1) Changed: Typos...
(2) Fixed: Corrected position of window for slice overlay window and
    orthogonality check.
(3) Changed: Changed path in slice overlay tool for saving image files to
    data folder.
(4) Changed: Disabled parallel processing for only one subject.

------------------------------------------------------------------------
r1521 | dahnke | 2019-11-21 20:01:03 +0100 (Thu, 21 Nov 2019) | 37 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_output.m
M       cat_main.m
M       cat_main_reportfig.m
M       cat_run.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m
M       cat_surf_info.m
A       cat_vbdist.m
A       cat_vol_downcut.m
A       cat_vol_eidist.m
A       cat_vol_eikonal3.m
A       cat_vol_genus0.m
A       cat_vol_interp3f.m
A       cat_vol_laplace3.m
A       cat_vol_laplace3R.m
A       cat_vol_localstat.m
A       cat_vol_median3.m
A       cat_vol_median3c.m
A       cat_vol_pbt2.m
M       cat_vol_pbtp.cpp
A       cat_vol_pbtp.m
M       cat_vol_simgrow.c
A       cat_vol_simgrow.m
M       tbx_cfg_cat.m

(1) Changed:    Added layer4 and myelination map output for developer
                in cat_surf_createCS.
(2) Changed:    Updated dependencies of the surfaces and textures in
                cat_conf_output, cat_main, cat_run (not full working).
(3) New:        Added reduce_mesh developer GUI variable to switch between
                SPM, MATLAB, and no surface reduction in cat_conf_extopts.
(4) New:        Added matlab help file for cat_vol_* c and c++ functions.


------------------------------------------------------------------------
r1520 | dahnke | 2019-11-19 22:52:09 +0100 (Tue, 19 Nov 2019) | 49 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_output.m
M       cat_defaults.m
M       cat_io_cmd.m
M       cat_main.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_stat_marks.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_display.m
M       cat_surf_fun.m
M       cat_surf_info.m
M       cat_surf_render2.m
M       cat_vol_pbt3.m
M       cat_vol_qa.m

(1) New:      Added two new runtime optimized collision corrections approaches in
              cat_surf_fun that were called in cat_surf_createCS2. The first approach
              (collcorr22) utilizes the CAT_selfintersect function that makes it
              relativ slow (15 minutes), whereas the second approach (collcorr23) uses
              the relative position map of PBT that makes it quite fast (2 minutes) but
              less accurate. There is also an extended version (collcorr24) that
              optimize the surface based on the Ypp map and an even more accurate
              version (collcorr25) that combines collcorr22 and collcorr24.
(2) Changed:  Updated extended expert options for mesh resolution and collision
              correction in cat_conf_extopts.
(3) Changed:  Many corrections and updates in cat_surf_createCS2 and cat_surf_fun that
              support the new self-intersection corrections and the evaluation of
              surface reconstruction. Small adaptions of cat_surf_createCS to support
              the surface reconstruction measures but not for collision correction.
(4) Changed:  Added output for surface measures in cat_main, cat_main_reportstr,
              cat_main_reportfig, and cat_stat_marks.
(5) Fixed:    Corrected atlas colormap naming bug, texture and surface handling in
              cat_surf_render2. Little changes for PNG output.
(6) New:      Added expert output options for the percentage position map and surface
              measures in cat_conf_output, cat_defaults, and cat_surf_createCS2.
(7) Fixed:    Corrected setting in cerebellar surface reconstruction and added
              'cb' definition for reconstruction of both sides in cat_surf_info,
              cat_main, cat_surf_display, and cat_main_createCS2.
              Added standard resolution full cerebellar average surfaces 'cb.*'.
(8) Fixed:    Corrected output of surface defect maps in cat_surf_createCS2
              and added settings to cat_surf_info and cat_surf_render2.
(9) New:      Added improved version of PBT (cat_surf_pbt2 and 3).



------------------------------------------------------------------------
r1519 | gaser | 2019-11-19 11:48:29 +0100 (Tue, 19 Nov 2019) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_catsimple.m
M       cat_conf_long.m
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_simple.m
M       cat_vol_qa.m
M       html/cat.html
M       tbx_cfg_cat.m

Changed: Added suggestions by Guillaume Flandin to make CAT12 conform to Octave.

------------------------------------------------------------------------
r1518 | gaser | 2019-11-13 12:27:46 +0100 (Wed, 13 Nov 2019) | 31 lines

Changed paths:
M       CHANGES.txt
M       Makefile
D       cat_batch_resample_standalone.m
        > moved to standalone/cat_standalone_resample.txt
D       cat_batch_simple_standalone.m
        > moved to standalone/cat_standalone_simple.txt
D       cat_batch_standalone.m
        > moved to standalone/cat_standalone_segment.txt
D       cat_batch_standalone.sh
        > moved to standalone/cat_standalone.sh
D       cat_parallelize.sh
        > moved to standalone/cat_parallelize.sh
A       standalone
A  +    standalone/cat_parallelize.sh
        > moved from cat_parallelize.sh
A  +    standalone/cat_standalone.sh
        > moved from cat_batch_standalone.sh
A  +    standalone/cat_standalone_resample.txt
        > moved from cat_batch_resample_standalone.m
A  +    standalone/cat_standalone_segment.txt
        > moved from cat_batch_standalone.m
A  +    standalone/cat_standalone_simple.txt
        > moved from cat_batch_simple_standalone.m
A       standalone/cat_standalone_smooth.txt

(1) Changed: Moved standalone functions to separate folder "standalone" and
    renamed files to begin with "cat_standalone".
(2) Changed: Added option to define two additional arguments for
    cat_standalone.sh.

------------------------------------------------------------------------
r1517 | gaser | 2019-11-12 14:47:37 +0100 (Tue, 12 Nov 2019) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
!       VBM12-Manual_Japanese.doc
!       VBM12-Manual_Japanese.pdf
M       cat12.m
M       html/cat.html
M       spm_cat12.m

(1) Fixed: Removed forced use of nox-expert mode for standalone installation in
    spm_cat12.m
(2) Changed: Disable switch to beginners mode in GUI fpr standalone
    installations.

------------------------------------------------------------------------
r1516 | gaser | 2019-11-12 00:14:48 +0100 (Tue, 12 Nov 2019) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_simple_standalone.m
M       cat_batch_standalone.m
M       cat_batch_standalone.sh
M       cat_defaults.m
M       spm_cat12.m
M       tbx_cfg_cat.m

(1) Changed: Call batch scripts for standalone installations always in expert
    mode to allow more options.
(2) Changed: Call CAt12 GUI for standalone installation in default (non-
    expert) mode.
(3) Change: Use surface extraction by default.


------------------------------------------------------------------------
r1515 | gaser | 2019-11-10 00:01:28 +0100 (Sun, 10 Nov 2019) | 27 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_cat.m
M       cat_batch_cat.sh
M       cat_batch_long.sh
A       cat_batch_resample_standalone.m
A       cat_batch_simple_standalone.m
M       cat_batch_spm.sh
A       cat_batch_standalone.m
A       cat_batch_standalone.sh
M       cat_conf_long.m
M       cat_conf_stools.m
M       cat_long_multi_run.m
A       cat_parallelize.sh
M       cat_simple.m
M       distribute_to_server.sh
M       html/cat.html

(1) Added: Shell script cat_batch_standalone.sh to call CAT!2 batch files for
    SPM12 standalone installation (e.g. for HPCs)
(2) Added: New batch modes for cat_batch_standalone.sh
(3) Added: Shell script cat_parallelize.sh to parallelize shell commands (e.g.
    cat_batch_standalone.sh).
(4) Fixed: Set number of processes to 0 for standalone (deployed) version.
(5) Changed: Extended input parameters for cat_batch_cat.m

------------------------------------------------------------------------
r1514 | gaser | 2019-10-28 07:42:00 +0100 (Mon, 28 Oct 2019) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_spm_preproc8.m
M       cat_spm_preproc_run.m
M       html/cat.html

Changed: Modified some setting according to the new SPM12 update in
cat_spm_preproc8.m and cat_spm_preproc_run.m.

------------------------------------------------------------------------
r1513 | gaser | 2019-10-17 15:46:13 +0200 (Thu, 17 Oct 2019) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_results.m

(1) Fixed: Images were not saved in selected folder in cat_surf_results.m
(2) Changed: Some minor changes in output during surface extraction.

------------------------------------------------------------------------
r1512 | gaser | 2019-10-17 11:41:42 +0200 (Thu, 17 Oct 2019) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_conf_stoolsexp.m
M       cat_surf_fun.m
M       cat_surf_results.m

(1) Fixed: Updated text field for slider in cat_surf_results.m
(2) Changed: Some minor changes in help text and file selection fields.

------------------------------------------------------------------------
r1511 | gaser | 2019-10-16 13:43:11 +0200 (Wed, 16 Oct 2019) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       html/cat.html

(1) Fixed: Field createCS_resampled was not correctly handled in
    cat_surf_createCS.m and cat_surf_createCS2.m.
(2) Changed: Some minor edits in help text.

------------------------------------------------------------------------
r1510 | gaser | 2019-10-16 12:12:29 +0200 (Wed, 16 Oct 2019) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_cat.m
M       cat_conf_extopts.m
M       cat_surf_createCS.m
MM      cat_surf_createCS2.m
M       html/cat.html
M       html/cat_starting.html

(1) Fixed: Added loadSurf function to cat_surf_createCS.m
(2) Fixed: Added CAT_SelfIntersect binaries.
(3) Fixed: Added new fields to cat_batch_cat.m to suppress warnings.
(4) Changed: Some minor edits in help text.

------------------------------------------------------------------------
r1509 | dahnke | 2019-09-30 10:04:07 +0200 (Mon, 30 Sep 2019) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m
M       cat_vol_partvol.m

(1) Fixed:   Corrected bugs in surface evaluation in cat_surf_fun and
             cat_surf_createCS(2).
(2) Fixed:   Corrected problems with to aggressive skull-stripping due to bad
             settings in cat_vol_partvol and cat_main_cleanup_gwc.


------------------------------------------------------------------------
r1508 | dahnke | 2019-09-27 14:20:01 +0200 (Fri, 27 Sep 2019) | 29 lines

Changed paths:
M       CHANGES.txt
M       cat_check_system_output.m
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
M       cat_surf_createCS.m
M       cat_surf_createCS2.m
M       cat_surf_fun.m
M       cat_surf_render2.m
M       cat_surf_resamp.m
M       cat_vol_partvol.m
M       development/Template_2_IXI555_MNI152_GS1mm.nii

(1) Changed:   Updated "collcorr" development parameter in cat_conf_extopts and
               added "vdist" parameter to control the mesh resolution. Updated
               also related settings and comments in cat_defaults.
(2) Changed:   Updated surface reconstruction settings in cat_main.
(3) Changed:   Added evaluation settings in cat_surf_createCS.
               Added output of white and pial surface.
(4) Changed:   Heavy updates in cat_surf_createCS.
(5) Changed:   Heavy updates in cat_surf_fun for the sub-functions cat_surf_evalCS,
               cat_surf_saveICO and cat_surf_collcorr.
(6) Changed:   Corrections in cat_surf_render2 to support menu entries for
               available (resampled) surfaces and further evaluation data files.
(7) Fixed:     Corrected setting for thalamus cutting for surface reconstruction
               in cat_vol_partvol.
(8) Fixed:     Tiny corrections in cat_check_system_output.

------------------------------------------------------------------------
r1507 | gaser | 2019-09-23 15:13:43 +0200 (Mon, 23 Sep 2019) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_opts.m
M       html/cat.html

(1) Changed: Moved "spm processing accuracy" option to expert mode.
(2) Fixed: Handling of font size in cat12.m was not correct.

------------------------------------------------------------------------
r1506 | gaser | 2019-09-13 12:20:58 +0200 (Fri, 13 Sep 2019) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_cat.m
M       cat_surf_createCS.m
A       cat_surf_createCS2.m

(1) Fixed: Suppress warning for longitudinal batch mode that is called from
    command shell.
(2) Changed: Moved new experimental cat_surf_createCS.m to cat_surf_createCS2.m
    and make the previous version again to the default cat_surf_createCS.m.

------------------------------------------------------------------------
r1505 | dahnke | 2019-09-12 18:17:33 +0200 (Thu, 12 Sep 2019) | 29 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_output.m
M       cat_defaults.m
M       cat_main.m
M       cat_surf_createCS.m
M       cat_surf_fun.m
M       cat_surf_info.m
M       cat_surf_render2.m
M       cat_vol_pbt.m

(1) Added collcorr parameter to control surface collision correction in
    cat_conf_extopts, cat_defaults, and cat_main.
(2) Cleaned cat_surf_createCS and removed fast-registration option of the
    developer mode in cat_surf_createCS. Add new collision correction.
    Changed order of functions to improve surface accuracy.
(3) Added new subfunction in cat_surf_fun to save surfaces and correct
    surface collisions.
(4) Added handling for pial, white, and layer4 surfaces in cat_surf_info
    and cat_surf_render2. Added surface info field to the menu.
(5) Limited search for surface and textures in cat_surf_render2 to a
    directory depth of 1.
(6) Small changes in the WM boundary optimization in cat_vol_pbt.





------------------------------------------------------------------------
r1504 | gaser | 2019-09-10 16:33:57 +0200 (Tue, 10 Sep 2019) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m
M       cg_io_send_to_server.m

Changed: Slightly changed deformation parameters in cat_surf_createCS.m.

------------------------------------------------------------------------
r1503 | gaser | 2019-09-06 17:18:48 +0200 (Fri, 06 Sep 2019) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_surf_createCS.m
M       html/cat.html

(1) Changed: Updated help text for stroke lesion tool.
(2) Changed: Deselected use of pial and WM surface for thickness estimation
    for experiemntal pial+WM surface creation in cat_surf_createCS.m.

------------------------------------------------------------------------
r1502 | gaser | 2019-09-04 11:03:30 +0200 (Wed, 04 Sep 2019) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_defaults.m
M       cat_surf_createCS.m
M       cat_surf_vol2surf.m
M       html/cat.html

(1) Fixed: Corrected deleting of temporary files in cat_surf_createCS.m for
    creation of pial and WM surface.
(2) Changed: Added automatically filling up of filenames if only 1 volume but
    multiple surfaces are given in cat_surf_vol2surf.m

------------------------------------------------------------------------
r1501 | gaser | 2019-09-02 09:29:29 +0200 (Mon, 02 Sep 2019) | 13 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_surf_createCS.m
M       cat_surf_vol2surf.m

(1) Fixed: Corrected print out of mapping points for volume to surface mapping
if only one mapping point was defined.
(2) Changed: Pial and WM surface are now using a corrected pbt image for better
and start at central surface to prevent intersections and obtain better surface
estimation in cat_surf_createCS.m (experimental).


------------------------------------------------------------------------
r1500 | gaser | 2019-08-21 14:34:20 +0200 (Wed, 21 Aug 2019) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_createCS.m
M       html/cat.html

Changed: Slight optimization of parameters for surface pipeline in
cat_surf_createCS.m.


------------------------------------------------------------------------
r1499 | gaser | 2019-08-20 08:51:35 +0200 (Tue, 20 Aug 2019) | 21 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_conf_stoolsexp.m
M       cat_defaults.m
M       cat_main_reportfig.m
M       cat_surf_createCS.m
M       html/cat.html
M       html/cat_starting.html

(1) Changed: Changed recommendation and default for smoothing size to smaller
    values.
(2) Changed: Added thickness limit of 5mm similar to Freesurfer to surface
    pipeline.
    cat_surf_createCS.m.
(3) Fixed: Check whether new spm_ov_mesh.m from SPM12 update is available and
    skip skull overlay if not.
(4) Changed: Disabled new pbtlas correction because of instabilities for data
    with larger atrophy.

------------------------------------------------------------------------
r1498 | gaser | 2019-08-16 16:05:38 +0200 (Fri, 16 Aug 2019) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_run_newcatch.m
M       cat_surf_createCS.m
M       html/cat.html

(1) Changed: Optimized parameters for surface reconstruction in
    cat_surf_createCS.m.
(2) Changed: Updated and optimized creation of pial and white surface in
    cat_surf_createCS.m.
(3) Changed: Added further anonymization of filenames to cat_run_newcatch.m

------------------------------------------------------------------------
r1497 | gaser | 2019-08-15 16:28:31 +0200 (Thu, 15 Aug 2019) | 32 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_conf_extopts.m
M       cat_defaults.m
D       cat_io_send_to_server.m
        > moved to cg_io_send_to_server.m
M       cat_run_job.m
M       cat_run_newcatch.m
M       cat_surf_createCS.m
M       cat_surf_vol2surf.m
M       cat_vol_pbt.m
A  +    cg_io_send_to_server.m
        > moved from cat_io_send_to_server.m
M       html/cat.html
M       spm_cat12.m

(1) Changed: Removed check for self-intersections because this was too slow.
(2) Changed: Anonymize filenames in error messages that are send to the SBM
    server. Furthermore categorize reports in finished|errors to get a better
    overview.
(3) Changed: Added again flag new_release to better control some of the new
    functions in cat_surf_createCS.m.
(4) Changed: Changed parameters for initial CAT_Central2Pial and CAT_RefineMesh
    in cat_surf_createCS.m.
(5) Changed: Anonymize filename in error message that is send to SBM server.
(6) Changed: Set interpolation to new "optimal" setting in cat_defaults.m.
(7) Fixed: Corrected some typos.
(8) Fixed: Corrected error with exist command in cat_surf_vol2surf.m


------------------------------------------------------------------------
r1496 | dahnke | 2019-08-15 15:40:32 +0200 (Thu, 15 Aug 2019) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_run_job.m
M       cat_surf_createCS.m
M       cat_vol_pbt.m

(1) Changed:  Small corrections in cat_vol_pbt.
(2) Fixed:    Added thickness estimation to the fast pipeline.
(3) New:      Added new 'optimal' resolution setting.


------------------------------------------------------------------------
r1495 | gaser | 2019-08-14 18:18:11 +0200 (Wed, 14 Aug 2019) | 23 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_defaults.m
M       cat_surf_createCS.m
M       cat_surf_resamp.m
M       cat_surf_vol2surf.m
M       html/cat.html
 M      html/cat_statistics.html

(1) Changed: Implemented Freesurfer distance method Tfs, which is using the mean
    of the closest distances between surf1-surf2 and surf2-surf1. This reduces
    occurance of larger thickness values. For mapping the files ?h.pbt.* can be
    still used which are the old thickness metrics from PBT and are more
    appropriate for mapping 3D measures.
(2) Changed: cat_createCS is now using some experimental features that were
    enabled before with the flag new_release. This includes check for self-
    intersection during surface refinement and mny smaller improvements during
    that step.
(3) Added: Added CAT binary CAT_SurfDistance which is estimating the new FS
    distance measure.


------------------------------------------------------------------------
r1494 | gaser | 2019-08-12 13:37:38 +0200 (Mon, 12 Aug 2019) | 18 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_main_reportfig.m
M       cat_stat_spm.m
M       cat_surf_parameters.m
M       cat_vol_pbt.m
M       html/cat.html
M       html/cat_statistics.html
M       html/images/CAT.png

(1) Fixed: Added global function to cat_stat_spm.m
(2) Fixed: Corrected typos and updated help text.


------------------------------------------------------------------------
r1493 | dahnke | 2019-08-12 12:09:42 +0200 (Mon, 12 Aug 2019) | 30 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_io_checkdepfiles.m
M       cat_io_report.m
M       cat_main.m
M       cat_main_reportfig.m
M       cat_surf_calc.m
M       cat_surf_createCS.m
M       cat_surf_fun.m
M       cat_surf_info.m
M       cat_surf_parameters.m
M       cat_surf_render2.m
M       cat_vol_pbt.m

(1) Fixed:    Corrected process bar output in cat_surf_calc.
(2) Fixed:    Small corrections in cat_surf_render2 to save images.
(3) Fixed:    Added further try-catch blocks for spm_orthviews and
              spm_ov_mesh in cat_main_reportfig and cat_io_report.
(4) Fixed:    Corrected bugs in cat_io_checkdepfiles.
(5) Changed:  Switch area-function code.
(6) New:      Added pbtlas to avoid thickness underestimation in
              strongly myelinated regions. Changes in cat_vol_pbt
              but also in cat_surf_createCS, cat_conf_extopts, cat_defaults.
(7) Fixed:    Added work-around for silly surface reconstruction error.
(8) New:      Added new thickness metrics to cat_surf_parameter,
              cat_surf_fun, and cat_conf_stools.

------------------------------------------------------------------------
r1492 | gaser | 2019-08-02 07:55:19 +0200 (Fri, 02 Aug 2019) | 18 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_io_report.m
MM      cat_io_send_to_server.m
M       cat_run_newcatch.m
M       html/cat.html
M       html/cat.txt
M       html/cat_instruction_templates.html
M       html/cat_methods_FN.html
M       html/cat_methods_RBM.html
A       html/cat_statistics.html

(1) Fixed: Corrected some links in online help.
(2) Changed: Added html about CAT12 user statistics.
(3) Changed: Added more detailed error information to statistics.

------------------------------------------------------------------------
r1491 | gaser | 2019-07-31 14:46:14 +0200 (Wed, 31 Jul 2019) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_catsimple.m
M       cat_main_reportfig.m
M       cat_run_newcatch.m
M       html/cat.html

(1) Fixed: Added try function to urlread in case that websever is down.
(2) Changed: Removed use of mac-address to create uniqe user id.

------------------------------------------------------------------------
r1490 | gaser | 2019-07-31 09:50:15 +0200 (Wed, 31 Jul 2019) | 24 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_batch_cat.m
M       cat_defaults.m
M       cat_io_report.m
A       cat_io_send_to_server.m
M       cat_main_reportfig.m
M       cat_plot_boxplot.m
M       cat_run_newcatch.m
M       html/cat.html
M       html/cat.txt
D       html/cat_ackknowledgement.html
        > moved to html/cat_acknowledgement.html
A  +    html/cat_acknowledgement.html
        > moved from html/cat_ackknowledgement.html

(1) Fixed: Many typos...
(2) Changed: Added image tracker to provide statistics about Matlab and CAT12
    versions and (un)successful preprocessings.
(3) Changed: Added cat.extopts.send_info flag to control sending of statistics
    tp SBM server.

------------------------------------------------------------------------
r1489 | gaser | 2019-07-02 11:29:46 +0200 (Tue, 02 Jul 2019) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_main_reportfig.m
M       cat_stat_check_cov.m
M       cat_stat_check_cov2.m
M       cat_surf_results.m

(1) Fixed: Corrected use of handles for older Matlab versions.
(2) Fixed: Checkbox for vilonplot in cat_stat_check_cov* disappeared.

------------------------------------------------------------------------
r1488 | gaser | 2019-07-01 22:58:14 +0200 (Mon, 01 Jul 2019) | 27 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_cat.m
M       cat_conf_extopts.m
M       cat_conf_stools.m
M       cat_io_writenii.m
M       cat_main_LAS2.m
M       cat_main_reportfig.m
M       cat_run_job.m
M       cat_stat_check_cov.m
M       cat_stat_check_cov2.m
M       cat_stat_diff.m
M       cat_surf_resamp.m
M       cat_update.m
M       html/cat.html

(1) Fixed: Missing deblank in cat_surf_resamp for checking files.
(2) Fixed: cat_stat_diff crashed in command line modus due to uncorrect
    indexing.
(3) Changed: Renamed some axes in cat_stat_check_cov.m for better description.
(4) Changed: Changed fontsize and content for image and colorbar title in
    cat_main_reportfig.m.
(5) Changed: Added lazy-option to expert mode.
(6) Fixed: Suppress warnings for uninitialized parameters in cat_batch_cat.m
(7) Fixed: Division by zero in cat_run_job.m.

------------------------------------------------------------------------
r1487 | gaser | 2019-06-19 14:22:23 +0200 (Wed, 19 Jun 2019) | 7 lines

Changed paths:
M       CHANGES.txt
M       templates_1.50mm/neuromorphometrics.csv

Fixed: Corrected atlas names for Neuromorphometrics atlas (thanks to Christina
Mundinger for pointing to this issue).

------------------------------------------------------------------------
r1486 | gaser | 2019-06-19 13:31:55 +0200 (Wed, 19 Jun 2019) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
 M      templates_1.50mm/TPM_Age11.5.nii

Changed: Added button to change user mode in CAT12 GUI.

------------------------------------------------------------------------
r1485 | gaser | 2019-06-18 18:02:09 +0200 (Tue, 18 Jun 2019) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_ROI.m
M       cat_conf_catsimple.m
M       cat_conf_long.m
M       cat_simple.m
M       tbx_cfg_cat.m

Fixed: Many changes and additional options to cat_*simple.m that should now run
for cross-sectional data without errors.

------------------------------------------------------------------------
r1484 | gaser | 2019-06-18 00:21:03 +0200 (Tue, 18 Jun 2019) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_catsimple.m
M       cat_simple.m

Changed: Added fields for smoothing to cat_*simple.m.

------------------------------------------------------------------------
r1483 | gaser | 2019-06-17 17:29:33 +0200 (Mon, 17 Jun 2019) | 18 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_catsimple.m
M       cat_defaults.m
M       cat_io_xml.m
M       cat_plot_boxplot.m
M       cat_simple.m
M       cat_surf_create_TPM_hull_surface.m
M       html/cat.html
A       templates_1.50mm/TPM_Age11.5.nii

(1) Added: Children template from NIH study with 11.5 years mean age.
(2) Changed: Updated preprocessing stream for simple preprocessing.
(3) Changed: Chnaged CAT12 default to ignore errors.
(4) Fixed: Overlay of hull surface for skull-stripped brains was not
    working in cat_surf_create_TPM_hull_surface.m

------------------------------------------------------------------------
r1482 | gaser | 2019-06-17 08:43:52 +0200 (Mon, 17 Jun 2019) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_io_xml.m
M       cat_surf_results.m
M       tbx_cfg_cat.m

(1) Fixed: For deployed versions number of cores is automatically set to 0.
(2) Changed: Initialization in cat12.m is called only for the first call of
    cat12.
(3) Fixed: Updated cat_io_xml.m to support deployed versions.
(4) Changed: Ticklength andGui entries modified in cat_surf_results.m

------------------------------------------------------------------------
r1481 | gaser | 2019-06-15 14:55:32 +0200 (Sat, 15 Jun 2019) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat12.m

(1) Fixed: Old cat12 windows were not closed.
(2) Fixed: Changed use of image handles in cat12.m

------------------------------------------------------------------------
r1480 | dahnke | 2019-06-06 12:48:36 +0200 (Thu, 06 Jun 2019) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_long_main.m
M       cat_long_multi_run.m
M       cat_parallelize.m
M       cat_simple.m

(1) Fixed:    Added resolution update of menu box elements.
(2) Fixed:    Corrected bug in cat_simple longitudinal preprocessing.




------------------------------------------------------------------------
r1479 | gaser | 2019-06-05 12:59:52 +0200 (Wed, 05 Jun 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_plot_boxplot.m

Changed: Added density plot and some predefined styles to cat_plot_boxplot.m

------------------------------------------------------------------------
r1478 | dahnke | 2019-06-04 18:19:06 +0200 (Tue, 04 Jun 2019) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_conf_stools.m
M       cat_long_main.m
M       cat_parallelize.m

(1) Fixed:    Corrected small things in the CAT menu.
(2) Fixed:    Corrected cat_parallelize output error.
(3) Fixed:    Improved cat_parallelize command line output.


------------------------------------------------------------------------
r1477 | gaser | 2019-06-03 10:18:29 +0200 (Mon, 03 Jun 2019) | 16 lines

Changed paths:
M       CHANGES.txt
 M      html/images/cat_bg.jpg
 M      html/images/cat_hd02.png
 M      html/images/cat_hd02blue.png
 M      html/images/cat_hd02blue2.png
 M      html/images/cat_hd02cyan.png
 M      html/images/cat_hd02green.png
 M      html/images/cat_hd02orange.png
 M      html/images/cat_hd02purple.png
 M      html/images/cat_hd02red.png
 M      html/images/cat_hd02yellow.png
M       templates_1.50mm/cobra.nii

Fixed; Cobra atlas had rounding issues with spm_atlas function.

------------------------------------------------------------------------
r1476 | gaser | 2019-05-31 22:14:11 +0200 (Fri, 31 May 2019) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat12.m

Changed: Disabled backgroundcolor to solve issues with older Matlab versions
for CAT12 GUI.

------------------------------------------------------------------------
r1475 | gaser | 2019-05-31 17:03:14 +0200 (Fri, 31 May 2019) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_long_multi_run.m
M       cat_stat_analyze_ROIs.m
RM      html/images/cat_bg.jpg
RM      html/images/cat_hd02blue.png
RM      html/images/cat_hd02blue2.png
RM      html/images/cat_hd02cyan.png
RM      html/images/cat_hd02green.png
RM      html/images/cat_hd02orange.png
RM      html/images/cat_hd02purple.png
RM      html/images/cat_hd02red.png
RM      html/images/cat_hd02yellow.png
 M      html/images/contact_small.jpg

(1) Changed: Updated CAT12 GUI.
(2) Changed: P-values of "0" are corrected to eps in cat_stat_analyze_ROIs.m

------------------------------------------------------------------------
r1474 | dahnke | 2019-05-31 16:16:12 +0200 (Fri, 31 May 2019) | 21 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_long_main.m
M       cat_parallelize.m
A       html/images/cat_bg.jpg
A       html/images/cat_hd02.png
A       html/images/cat_hd02blue.png
A       html/images/cat_hd02blue2.png
A       html/images/cat_hd02cyan.png
A       html/images/cat_hd02green.png
A       html/images/cat_hd02orange.png
A       html/images/cat_hd02purple.png
A       html/images/cat_hd02red.png
A       html/images/cat_hd02yellow.png

(1) Changed:    Added menu background images and add code to load them.
(2) Fixed:      Corrected batch loading functionality of cat_long_main.
(3) Fixed:      Corrections in cat_parallelize for correct DEP output
                that need further tests!

------------------------------------------------------------------------
r1473 | dahnke | 2019-05-31 12:38:06 +0200 (Fri, 31 May 2019) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_long_main.m
M       cat_long_multi_run.m
M       cat_parallelize.m
M       cat_run.m

(1) Changed:    Updated cat_run and cat_parallelize for MATLAB 2018 recommendations.
(2) Changed:    Added subject command line output batches and
                restructured cat_long_main.


------------------------------------------------------------------------
r1472 | gaser | 2019-05-29 22:11:33 +0200 (Wed, 29 May 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat12.m

Cosmetic changes in cat12.m

------------------------------------------------------------------------
r1471 | gaser | 2019-05-29 16:37:35 +0200 (Wed, 29 May 2019) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
MM      cat_io_checkdepfiles.m
MM      cat_simple.m
M       cat_update.m
M       html/cat.html

(1) Changed: Added version check to cat12.m
(2) Changed: Position of CAT12 GUI is now located right of SPM12 Graphic window
    and height of GUI is equal to SPM12 GUI.

------------------------------------------------------------------------
r1470 | gaser | 2019-05-29 13:49:16 +0200 (Wed, 29 May 2019) | 37 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_conf_long.m
M       cat_defaults.m
M       cat_install_tfce.m
MM      cat_run1445/cat_conf_ROI1445.m
MM      cat_run1445/cat_conf_extopts1445.m
MM      cat_run1445/cat_conf_long1445.m
MM      cat_run1445/cat_conf_opts1445.m
MM      cat_run1445/cat_defaults1445.m
MM      cat_run1445/cat_get_defaults1445.m
MM      cat_run1445/cat_long_main1445.m
MM      cat_run1445/cat_long_multi_run1445.m
MM      cat_run1445/cat_main1445.m
MM      cat_run1445/cat_main_LAS1445.m
MM      cat_run1445/cat_main_gcut1445.m
MM      cat_run1445/cat_main_registration1445.m
MM      cat_run1445/cat_run1445.m
MM      cat_run1445/cat_run_job10701445.m
MM      cat_run1445/cat_run_job1445.m
MM      cat_run1445/cat_run_job_APP_init10701445.m
MM      cat_run1445/cat_run_newcatch1445.m
MM      cat_run1445/cat_surf_createCS1445.m
MM      cat_run1445/cat_vol_partvol1445.m
MM      cat_run1445/cat_vol_sanlm1445.m
M       cat_stat_diff.m
 M      html/cat_methods_catsimple.html
 M      html/images/cat_methods_catsimple.png
A       html/images/contact_small.jpg
MM      internal/cat_admin_create_estwrite_version.m
M       tbx_cfg_cat.m

(1) Changed: Initial version of new CAT12 GUI.
(2) Changed: Smalle edits of help functions.
(3) Fixed: Expert mode in longitudinal segmentation was not recognized.

------------------------------------------------------------------------
r1469 | dahnke | 2019-05-28 11:51:29 +0200 (Tue, 28 May 2019) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_io_checkdepfiles.m
M       cat_main_reportstr.m
M       cat_run.m
M       cat_run_job.m
M       tbx_cfg_cat.m

(1) Fixed:    Corrected tiny errors in cat_io_checkdepfiles, cat_run, and tbx_cfg_cat.


------------------------------------------------------------------------
r1468 | dahnke | 2019-05-23 10:54:45 +0200 (Thu, 23 May 2019) | 8 lines

Changed paths:
M       CHANGES.txt
MM      cat_conf_catsimple.m

(1) New:    Added function cat_io_checkdepfiles to remove files that do not exist.
(2) Fixed:  Define settings to support ignore_errors function in batch mode.
(3) Fixed:  Added missed cat_simple function.

------------------------------------------------------------------------
r1467 | dahnke | 2019-05-23 10:52:34 +0200 (Thu, 23 May 2019) | 15 lines

Changed paths:
M       CHANGES.txt
A       cat_io_checkdepfiles.m
M       cat_run.m
M       cat_run1445/cat_run1445.m
A       cat_simple.m
M       cat_stat_IQR.m
M       cat_stat_TIV.m
M       cat_surf_parameters.m
M       cat_surf_resamp.m

(1) New:    Added function cat_io_checkdepfiles to remove files that do not exist.
(2) Fixed:  Define settings to support ignore_errors function in batch mode.
(3) Fixed:  Added missed cat_simple function.

------------------------------------------------------------------------
r1466 | gaser | 2019-05-23 10:20:13 +0200 (Thu, 23 May 2019) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_catsimple.m
M       cat_parallelize.m
M       cat_sanlm.mexa64
M       cat_sanlm.mexmaci64
M       cat_sanlm.mexw64
M       cat_vol_slice_overlay.m
M       sanlm_float.c

(1) Fixed: Indexing in cat_parallelize.m was wrong.
(2) Changed: Added option to deselect atlas labeling for scripting
    cat_vol_slice_overlay.m
(3) Changed: Switched multi-threading in sanlm_float.c to pthread also for
    windows systems and added some code to lock/unlock processes.

------------------------------------------------------------------------
r1465 | dahnke | 2019-05-17 11:34:01 +0200 (Fri, 17 May 2019) | 28 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_ROI.m
M       cat_conf_catsimple.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_parallelize.m
M       cat_run1173/cat_conf_long1173.m
M       cat_run1173plus/cat_conf_long1173plus.m
M       cat_run1445/cat_conf_long1445.m
M       cat_surf_parameters.m
M       html/cat_methods_catsimple.html
M       html/images/cat_methods_catsimple.png
M       tbx_cfg_cat.m

(1) Fixed:    Corrected bugs in cat_simple and removed additional modality
              option from non-developer GUIs.
(2) New:      Added surface-based ROI processing in cat_simple batch.
(3) New:      Added ROI GUIs to cat_simple for experts.
(4) New:      Added surface atlases menu in cat_conf_ROI and default surface
              atlases to cat_defaults.
(5) Changed:  Renamed long1173(plus) batches.
(6) Fixed:    Renamed functions of TIV GUI that was similar as the called
              function name and caused error in batch processing.
(7) Fixed:    Corrected small bugs in cat_parallelize.



------------------------------------------------------------------------
r1464 | dahnke | 2019-05-15 09:34:04 +0200 (Wed, 15 May 2019) | 50 lines

Changed paths:
M       CHANGES.txt
A       cat_conf_catsimple.m
M       cat_conf_long.m
M       cat_conf_output.m
M       cat_long_main.m
M       cat_long_multi_run.m
M       cat_run.m
A       cat_run1445
A       cat_run1445/cat_conf_ROI1445.m
A       cat_run1445/cat_conf_extopts1445.m
A       cat_run1445/cat_conf_long1445.m
A       cat_run1445/cat_conf_opts1445.m
A       cat_run1445/cat_defaults1445.m
A       cat_run1445/cat_get_defaults1445.m
A       cat_run1445/cat_long_main1445.m
A       cat_run1445/cat_long_multi_run1445.m
A       cat_run1445/cat_main1445.m
A       cat_run1445/cat_main_LAS1445.m
A       cat_run1445/cat_main_gcut1445.m
A       cat_run1445/cat_main_registration1445.m
A       cat_run1445/cat_run1445.m
A       cat_run1445/cat_run_job10701445.m
A       cat_run1445/cat_run_job1445.m
A       cat_run1445/cat_run_job_APP_init10701445.m
A       cat_run1445/cat_run_newcatch1445.m
A       cat_run1445/cat_surf_createCS1445.m
A       cat_run1445/cat_vol_partvol1445.m
A       cat_run1445/cat_vol_sanlm1445.m
M       cat_surf_parameters.m
M       cat_version.m
A       html/cat_methods_catsimple.html
A       html/images/cat_methods_catsimple.png
A       internal/cat_admin_create_estwrite_version.m
M       tbx_cfg_cat.m

(1) New:    Added parameter for output of tissue class 4 to 6 on the experts GUI.
(2) New:    Added batch dependencies for catreport pdf, catreport jpg and catlog.txt
            in tbx_cfg_cat and cat_run.
(3) Fixed:  Small corrections in cat_run for developer parameters.
(4) New:    Added stable subversion of the preprocessing (1445) and the internal
            script cat_admin_create_estwrite_version that creates it.
(5) New:    Added cat_simple batch and function.
(6) New:    Added parameter and dependency for cat_simple batch in cat_long_main,
            cat_long_multi_run and cat_conf_long.
(7) Fixed:  Create output in cat_surf_parameters even if no measure is selected.
(8) New:    Added date variable to the output of cat_version.



------------------------------------------------------------------------
r1463 | dahnke | 2019-05-07 18:02:24 +0200 (Tue, 07 May 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m

(1) Fixed:   Corrected bug in cat_surf_results.

------------------------------------------------------------------------
r1462 | dahnke | 2019-05-07 17:51:06 +0200 (Tue, 07 May 2019) | 24 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_parallelize.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_calc.m
M       cat_surf_flipsides.m
M       cat_surf_render2.m
M       cat_surf_resamp.m
M       cat_surf_results.m
M       cat_vol_slice_overlay.m

(1) Changed:     Reorganization of the cat_conf_stools and cat_conf_tools
                 files by creating sub-functions for each batch.
(2) Changed:     Updated documentation of cat_surf_flip.
(3) Changed:     Switched to sample input in cat_surf_resamp.
(4) Changed:     Added batch outputs for cat_surf_calc(sub) and added
                 possibility to create average data of multiple subjects.
(5) Fixed:       Corrected tiny bugs in cat_parallelize, cat_surf_render2,
                 and cat_stat_analyze_ROIs, cat_vol_slice_overlay.
(6) New:         Added histogram output functions in cat_surf_results.


------------------------------------------------------------------------
r1461 | gaser | 2019-05-03 14:10:21 +0200 (Fri, 03 May 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_calc.m

Fixed: Replaced use of "contains" by strfind to be compatible to older versions.

------------------------------------------------------------------------
r1460 | gaser | 2019-05-03 14:09:17 +0200 (Fri, 03 May 2019) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_extopts.m
M       cat_conf_stools.m
M       cat_surf_fun.m
M       cat_surf_resamp.m
M       cat_surf_results.m
M       html/cat.html

(1) Changed: Some cosmetic changes and correction of typos.
(2) Fixed: Replaced use of "contains" by strfind to be compatible to older
    versions.

------------------------------------------------------------------------
r1459 | dahnke | 2019-04-29 15:03:46 +0200 (Mon, 29 Apr 2019) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_surf_fun.m
M       cat_surf_parameters.m
M       cat_surf_resamp.m

1) Fixed:  Corrected surface-based GM volume estimation in cat_surf_fun.

------------------------------------------------------------------------
r1458 | dahnke | 2019-04-29 13:07:25 +0200 (Mon, 29 Apr 2019) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_surf_info.m
M       cat_surf_results.m

1) Fixed:  Corrected dependencies in cat_surf_results batch.

------------------------------------------------------------------------
r1457 | dahnke | 2019-04-29 12:16:31 +0200 (Mon, 29 Apr 2019) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_surf_fun.m
M       cat_surf_info.m
M       cat_surf_parameters.m
M       cat_surf_results.m

1) New:  Added batch mode for cat_surf_results.
2) New:  Added GM volume estimation for surfaces in cat_surf_parameters
         (not ready right now).


------------------------------------------------------------------------
r1456 | dahnke | 2019-04-27 14:49:26 +0200 (Sat, 27 Apr 2019) | 24 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_surf_GI3D.m
M       cat_surf_calc.m
M       cat_surf_epivolsurf.m
M       cat_surf_fun.m
M       cat_surf_gyrification.m
M       cat_surf_info.m
M       cat_surf_parameters.m
M       cat_surf_render2.m
M       cat_surf_resamp.m

1) Fixed:     Corrected small bugs in cat_surf_parameter, cat_surf_fun,
              cat_surf_gyrification, cat_surf_info, and cat_surf_epivolsurf.
              Removed old commented code in cat_surf_epivolsurf.
2) Fixed:     Corrected mesh bug in cat_surf_calc.
3) Changed:   Renamed "inner" to "white" and "outer" to "pial" surface.
4) Changed:	  Added lazy mode in cat_surf_resamp in developer mode.
5) New:       Added "synchronies views" option for textures in cat_surf_render2.
6) New:       Added area mapping schema in cat_surf_fun & cat_surf_parameters.



------------------------------------------------------------------------
r1455 | gaser | 2019-04-24 14:54:26 +0200 (Wed, 24 Apr 2019) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_defaults.m
M       cat_stat_check_SPM.m
M       cat_stat_check_cov.m
M       cat_surf_results.m
M       html/style.css

(1) Changed: Added option for default GUI font size to cat_defaults and changed
    the resp. GUI functions to use this option.
(2) Changed: Also use now dynamic font size for hmtl online help.

------------------------------------------------------------------------
r1454 | gaser | 2019-04-24 12:36:34 +0200 (Wed, 24 Apr 2019) | 19 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_tools.m
M       cat_main.m
M       cat_main_reportfig.m
M       cat_stat_check_cov.m
M       cat_surf_results.m
M       cat_vol_qa.m
M       html/cat.html
M       html/cat.txt
M       html/cat_FAQ.html
M       html/cat_methods.html
M       html/cat_tools_checkcov.html

(1) Changed: Updated online help.
(2) Changed: Updated font sizes in cat_surf_results.m
(3) Fixed: Corrected typos in cat_stat_check_cov.m that caused crashes.

------------------------------------------------------------------------
r1453 | gaser | 2019-04-23 22:18:53 +0200 (Tue, 23 Apr 2019) | 25 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_conf_extopts.m
M       cat_main_registration.m
M       cat_main_registration2.m
M       cat_main_reportfig.m
M       cat_parallelize.m
M       cat_stat_check_SPM.m
M       cat_stat_check_cov.m
M       cat_surf_GI3D.m
M       cat_surf_results.m
M       cat_tst_cattest.m
M       html/cat_FAQ.html
M       html/cat_methods_VBM.html
M       templates_1.50mm/anatomy.txt

(1) Changed: Updated online help.
(2) Changed: Updated font sizes in cat12.m, cat_surf_results.m, and
    cat_stat_check_cov.m
(3) Fixed: Suppress warnings in parallelization.
(4) Fixed. Check that spm12 update was successful in cat_main_reportfig.m
(5) Changed: Changed name of standard APP from "rough" to "default".
(6) Changed: Shortened several menu entries.

------------------------------------------------------------------------
r1452 | dahnke | 2019-04-17 18:10:54 +0200 (Wed, 17 Apr 2019) | 39 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_io_updateStruct.m
M       cat_parallelize.m
M       cat_surf_epivolsurf.m
M       cat_surf_fun.m
M       cat_surf_gyrification.m
M       cat_surf_info.m
M       cat_surf_parameters.m
M       cat_surf_render2.m
M       cat_surf_resamp.m
!       development
!       development/Template_0_IXI555_MNI152_GS1mm.nii
!       development/Template_1_IXI555_MNI152_GS1mm.nii
!       development/Template_2_IXI555_MNI152_GS1mm.nii
!       development/Template_3_IXI555_MNI152_GS1mm.nii
!       development/Template_4_IXI555_MNI152_GS1mm.nii
!       development/Template_4_IXI555_MNI152_GS1mm_corr.nii
!       development/cat.nii
!       development/cat_main_LAS.m
!       development/cat_surf_createCS.m
!       development/cat_vol_average.m

1) Docu:      Added comments in cat_parallelize.
2) Fixed:     Added missed for-loop in cat_parallelize.
3) Fixed:     Corrected small problems in cat_surf_epivolsurf.
4) Fixed:     Corrected texture detection problems for 32k surfaces in cat_surf_render2.
5) Changed:   Try to improve volume to surface render function in cat_surf_fun.
6) New:       Added expert GUI for iGI and oGI development in cat_conf_stools.
7) New:       Updated GI functions in cat_surf_gyrification.
8) New:       Added GI help functions in cat_surf_fun to estimate the core.
9) Deleted:   Removed multiple non-validated gyrification measures in cat_conf_stools,
              cat_surf_parameters and cat_surf_gyrification.




------------------------------------------------------------------------
r1451 | dahnke | 2019-04-04 10:49:28 +0200 (Thu, 04 Apr 2019) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_GI3D.m
M       cat_surf_epivolsurf.m
M       cat_surf_fun.m
M       cat_surf_gyrification.m
M       cat_surf_render2.m

1) Fixed:   Corrected small bugs in cat_surf_parameter and related functions.

------------------------------------------------------------------------
r1450 | gaser | 2019-04-04 04:11:14 +0200 (Thu, 04 Apr 2019) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main_registration.m
M       cat_surf_results.m
M       cat_vol_slice_overlay.m
M       html/cat.html

(1) Changed: Handling of clipped values has changed and saved images are now
    cropped to get rid of unnecessary background in cat_surf_results.m.
(2) Fixed: Colorbar Ticks were shifted for slice overlay.

------------------------------------------------------------------------
r1449 | dahnke | 2019-04-03 13:34:20 +0200 (Wed, 03 Apr 2019) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_io_cmd.m
M       cat_main_write.m
M       cat_parallelize.m

1) Fixed:   Tried to correct dependency handling in cat_parallelize.
2) Fixed: 	Tried to fix Gabriels server IO error in cat_io_cmd.

------------------------------------------------------------------------
r1448 | gaser | 2019-04-03 02:43:59 +0200 (Wed, 03 Apr 2019) | 17 lines

Changed paths:
D       CAT12-Manual-GoogleDocs.webloc
M       CHANGES.txt
M       Contents.m
M       cat_main_reportfig.m
M       cat_stat_analyze_ROIs.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_ui.m
M       html/cat.html

(1) Fixed: Catched overlay error in cat_main_reportfig.m and print advice to
    updated SPM12.
(2) Fixed: For analyzing ROIs global scaling was not considered correctly.
(3) Fixed: If no results were displayed unlinking of files was not correct
    for analyzing ROIs.
(4) Changed: Added option for atlas labeling to slice overlay.

------------------------------------------------------------------------
r1447 | gaser | 2019-03-31 23:03:39 +0200 (Sun, 31 Mar 2019) | 13 lines

Changed paths:
A       CAT12-Manual-GoogleDocs.webloc
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_stat_analyze_ROIs.m
M       html/cat.html
M       spm_cat12.m

(1) Fixed: Corrected error in cat_stat_analyze_ROIs.m if no xml-files were found.
(2) Added: GoogleDoc fpr CAT12 manual.
(3) Changed: Updated version information.

------------------------------------------------------------------------
r1446 | dahnke | 2019-03-26 17:43:53 +0100 (Tue, 26 Mar 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m

*) Fixed:   Corrected handling of cat_main_registration(2).

------------------------------------------------------------------------
r1445 | gaser | 2019-03-22 16:11:31 +0100 (Fri, 22 Mar 2019) | 7 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       html/cat_versions.html

Changed: Updated version information.

------------------------------------------------------------------------
r1444 | gaser | 2019-03-22 15:30:35 +0100 (Fri, 22 Mar 2019) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_long_main.m
M       cat_vol_groupwise_ls.m
M       cat_vol_series_align.m

(1) Fixed: Regularization for non-linear registration in longitudinal registration
    was dependent on signal. Now the images are internally scaled to a constant
    global mean value.
(2) Changed: Corrected regularization fir intra-subject bias correction in
    longitudinal pipeline.

------------------------------------------------------------------------
r1443 | gaser | 2019-03-21 16:15:33 +0100 (Thu, 21 Mar 2019) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_long.m
M       cat_conf_tools.m
M       cat_long_main.m
M       cat_parallelize.m
M       cat_vol_groupwise_ls.m
M       cat_vol_series_align.m
M       tbx_cfg_cat.m

Changed: Increased regularization for intra-subject bias correction in longitudinal
registration.

------------------------------------------------------------------------
r1442 | dahnke | 2019-03-21 08:48:36 +0100 (Thu, 21 Mar 2019) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_parallelize.m
M       cat_vol_ctype.m

*) Fixed:   Corrected bugs in cat_parallelize and cat_vol_ctype.


------------------------------------------------------------------------
r1441 | gaser | 2019-03-20 16:24:06 +0100 (Wed, 20 Mar 2019) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_long_main.m

Changed: Increased regularization for intra-subject bias correction in longitudinal
registration.

------------------------------------------------------------------------
r1440 | gaser | 2019-03-20 10:21:59 +0100 (Wed, 20 Mar 2019) | 8 lines

Changed paths:
M       CHANGES.txt
MM      cat_conf_output.m
M       cat_vol_sanlm.m

Fixed: Corrected bug in cat_vol_sanlm for direct call of input is not single
format.

------------------------------------------------------------------------
r1439 | gaser | 2019-03-20 10:09:26 +0100 (Wed, 20 Mar 2019) | 27 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_long.m
M       cat_conf_output.m
M       cat_long_main.m
M       cat_parallelize.m
M       cat_run.m
M       html/cat.html
M       tbx_cfg_cat.m
 M      templates_animals/baboon_T1.nii
 M      templates_animals/baboon_TPM.nii
 M      templates_animals/baboon_Template_1.nii
 M      templates_animals/baboon_Template_2.nii
 M      templates_animals/baboon_Template_3.nii
 M      templates_animals/baboon_Template_4.nii
 M      templates_animals/baboon_Template_5.nii
 M      templates_animals/baboon_Template_6.nii
 M      templates_animals/baboon_brainmask.nii
 M      templates_animals/baboon_cat.nii

(1) Changed: Output conf options are now removed from tbx_cfg_cat.m and will be
    called from cat_conf_output.m.
(2) Changed: Default bias corrected output in CAT12 is now indicated as
    normalized image and the original structure of the variable bias is now used.


------------------------------------------------------------------------
r1438 | dahnke | 2019-03-19 16:38:26 +0100 (Tue, 19 Mar 2019) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_long.m
A       cat_conf_output.m
M       cat_parallelize.m
M       cat_run.m

*) Fixed: 	Corrected dependencies of the longitudinal batch.

------------------------------------------------------------------------
r1437 | gaser | 2019-03-12 12:00:31 +0100 (Tue, 12 Mar 2019) | 13 lines

Changed paths:
M       CHANGES.txt
M       html/cat_methods_QA.html
M       html/cat_methods_RBM.html
M       html/cat_methods_SBM.html
M       html/cat_methods_VBM.html
M       html/cat_methods_validation.html
M       html/cat_tools_SBM.html
M       html/cat_tools_VBM.html
M       html/cat_tools_checkcov.html

Fixed: Corrected http addresses in online help to https.

------------------------------------------------------------------------
r1436 | gaser | 2019-03-06 17:46:15 +0100 (Wed, 06 Mar 2019) | 42 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_main_LAS2.m
M       cat_run1173/cat_vol_partvol1173.m
M       cat_stat_check_cov2.m
M       cat_stat_histth.m
M       cat_stat_marks.m
M       cat_vbdist.c
M       cat_vol_ROIval.c
M       cat_vol_atlas.m
M       cat_vol_correct_slice_scaling.m
M       cat_vol_downcut.c
M       cat_vol_eidist.c
M       cat_vol_eikonal3.c
M       cat_vol_genus0.c
M       cat_vol_gradient3.c
M       cat_vol_laplace3.c
M       cat_vol_laplace3R.c
M       cat_vol_localstat.c
M       cat_vol_median3.c
M       cat_vol_median3c.c
M       cat_vol_partvol.m
M       cat_vol_pbtp.cpp
M       cat_vol_pbtv.cpp
M       cat_vol_sanlm.m
M       cat_vol_simgrow.c
M       html/cat.html
M       html/cat_FAQ.html
M       html/cat_methods_RBM.html
M       html/cat_tools_VBM.html
M       html/cat_tools_checkcov.html
M       html/cat_tools_checkcov_exclusion.html
M       internal/cat_vol_atlas.m
M       templates_1.50mm/cobra.nii

(1) Fixed: Many typos...
(2) Changed: Removed udp options.

------------------------------------------------------------------------
r1435 | dahnke | 2019-03-06 12:24:38 +0100 (Wed, 06 Mar 2019) | 60 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_conf_extopts.m
M       cat_conf_long.m
M       cat_long_multi_run.m
M       cat_main.m
M       cat_main_APRG.m
M       cat_main_kamap.m
M       cat_main_registration.m
M       cat_main_registration2.m
M       cat_parallelize.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job_APRGs.m
M       cat_run_job_multiTPM.m
M       cat_spm_preproc8.m
M       cat_surf_createCS.m
M       cat_vol_ctype.m
M       spm_cat12.m
A       templates_animals/baboon_T1.nii
A       templates_animals/baboon_TPM.nii
A       templates_animals/baboon_Template_1.nii
A       templates_animals/baboon_Template_2.nii
A       templates_animals/baboon_Template_3.nii
A       templates_animals/baboon_Template_4.nii
A       templates_animals/baboon_Template_5.nii
A       templates_animals/baboon_Template_6.nii
A       templates_animals/baboon_brainmask.nii
A       templates_animals/baboon_cat.nii
M       templates_animals/chimpanzee_T1.nii
M       templates_animals/chimpanzee_TPM.nii
M       templates_animals/chimpanzee_atlas_davi.nii
M       templates_animals/chimpanzee_cat.nii

*) Fixed: 	Corrected tissue intensity settings in cat_run_job_APRGs (CRITICAL!).
*) New:     Added SPM job structure support for parallel preprocessing
            in cat_run and cat_parallelize.
*) New: 	Added parallel processing for longitudinal pipeline in cat_conf_long
            cat_long_multi_run.
*) New: 	Updated chimpanzee templates (TPM, T1, cat-atlas, davi-atlas).
*) New:		Added float32 and float64 definitions in cat_vol_ctype.
*) New: 	Added baboon and macaque cases in cat12 and templates (still in development).
*) Fixed: 	Corrections for general closing of the brainmask in cat_main_APRG.
*) Fixed: 	Corrections in cat_run_job to support full affine registration
			in primates. Added catch for spm_maffreg with less smoothing.
			Added additional try-catch block in case of a failed SPM
			preprocessing (spm_preproc8) with lower accuracy.
*) Fixed: 	Corrected tiny indices-errors in cat_run_job_multiTPM.
*) Fixed:   Corrected typos in cat_conf_extopts and cat_spm_preproc8.
*) Fixed: 	Additional turn off of the GIFTI warning in cat_surf_createCS.
*) Fixed:   Added more complex skull-stripping in cat_main_kamap.
*) Fixed:   Corrected fast registration operation in cat_main and added
            fast Dartel preprocessing option in cat_main_registration and
            cat_main_registration2.
*) Fixed:   Added final affine registration from cat_main_registration in
            cat_main_registration2.



------------------------------------------------------------------------
r1434 | gaser | 2019-02-28 11:32:08 +0100 (Thu, 28 Feb 2019) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_cat.m
M       cat_batch_long.m
M       html/cat.html

Fixed: Corrected typos in batch shell scripts.

------------------------------------------------------------------------
r1433 | gaser | 2019-02-27 16:52:49 +0100 (Wed, 27 Feb 2019) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_cat.m
M       cat_batch_long.m
M       cat_defaults.m
M       cat_vol_groupwise_ls.m
M       html/cat.html

(1) Changed: Again changed regularization for intra-subject bias correction which
    is now increased iteratively if local bias correction get too large.
(2) Changed: Added function for sending system information to SBM server for
    internal use. Also added option to diable this feature in cat_default.m.

------------------------------------------------------------------------
r1432 | gaser | 2019-02-22 17:18:04 +0100 (Fri, 22 Feb 2019) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_io_senderrormail.m
M       cat_vol_groupwise_ls.m

Changed: Changed regularization for intra-subject bias correction to make it
more robust for local artefacts.


------------------------------------------------------------------------
r1431 | gaser | 2019-02-21 14:51:35 +0100 (Thu, 21 Feb 2019) | 17 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_main_reportfig.m
M       cat_stat_check_cov2.m
M       cat_vol_groupwise_ls.m
M       html/cat.html
M       html/cat_versions.html

(1) Fixed: Corrected bug in cat_vol_groupwise_ls.m for longitudinal pipeline that
    caused NaN images for some data. Now the final intra-subject bias-correction
    don't uses a brainmask.
(2) Fixed: Uncorrect line breaks in cat_stat_check_cov2.m for help functions.
(3) Changed: Suppress annoying warning for longitudinal pipeline if called from
    command line.

------------------------------------------------------------------------
r1430 | gaser | 2019-02-19 17:01:28 +0100 (Tue, 19 Feb 2019) | 24 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_long_APP.m
M       cat_main_reportfig.m
M       cat_spm_preproc8.m
M       cat_stat_analyze_ROIs.m
M       cat_stat_check_cov.m
M       cat_stat_check_cov2.m
M       cat_surf_fun.m
M       cat_vol_atlas.m
M       html/cat.html
M       spm_cat12.m

(1) Fixed: Corrected bug in spm_cat12.m
(2) Fixed: Replaced many local paths in several files by generic spm12 folders.
(3) Changed: Added option to switch between violin and box plot in
    cat_stat_check_cov.m
(4) Changed: Better scaling for color map in cat_stat_check_cov.m
(5) Changed: Added printout of t/F value and Ze value for ROI analysis.
(6) Fixed: Added try-catch to deal with some unclear errors in cat_main_reportfig.m
(7) Changed: Inperpolation of brainmask for longitudinal pipeline is now bilinear
    to prevent issues with some data.

------------------------------------------------------------------------
r1429 | gaser | 2019-02-08 15:12:41 +0100 (Fri, 08 Feb 2019) | 7 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       html/cat_versions.html

Changed: Updated online help and CAT12 manual.

------------------------------------------------------------------------
r1428 | gaser | 2019-02-08 14:44:55 +0100 (Fri, 08 Feb 2019) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_analyze_ROIs.m
M       cat_stat_check_cov2.m
M       html/cat.html

(1) Changed: cat_stat_analyze_ROIs.m now better finds related xml-files and
    also corrects if multiple xml-files are found per data set.
(2) Fixed: Removed minor bug in cat_stat_check_cov2.m.

------------------------------------------------------------------------
r1427 | gaser | 2019-02-07 14:53:49 +0100 (Thu, 07 Feb 2019) | 18 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_conf_tools.m
M       cat_run.m
M       cat_stat_analyze_ROIs.m
M       cat_stat_check_SPM.m
M       cat_stat_check_cov2.m
M       cat_surf_parameters.m
M       cat_surf_results.m
M       html/cat.html

(1) Fixed: Removed some minor bugs in cat_surf_results.m, cat_surf_parameters.m,
    cat_stat_check_SPM.m, and cat_run.m.
(2) Fixed: Removed many bugs in cat_stat_check_cov2.m that were caused if no xml-
    files could be found.

------------------------------------------------------------------------
r1426 | gaser | 2019-02-04 12:51:40 +0100 (Mon, 04 Feb 2019) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_extopts.m
M       cat_long_multi_run.m
MM      cat_vol_avg.m
M       check_pipeline.sh
M       check_pipeline_ROIs.m
M       html/cat.html
M       html/cat_versions.html

(1) Changed: Updated information about version CAT12.6-rc1 in online help.
(2) Changed: Some minor changes in check_pipeline* code.

------------------------------------------------------------------------
r1425 | dahnke | 2019-02-01 15:50:22 +0100 (Fri, 01 Feb 2019) | 20 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_conf_extopts.m
M       cat_main.m
M       cat_main_APRG.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_run.m
M       cat_run_job_APRGs.m
M       cat_surf_createCS.m

1) Fixed:  Corrected registration menu behavior in cat_run and cat_conf_extopts.
2) Fixed:  Corrected problems in APRG skull-strippings cat_run_jobAPRGs and
           cat_main_APRG.
3) Fixed:  Corrected small typos in CAT report generation cat_main_reportstr.
4) Fixed:  Corrected small bugs in cat_surf_createCS.
5) Fixed:  Turned off GIFTI warning in cat12 script.


------------------------------------------------------------------------
r1424 | gaser | 2019-01-30 16:56:09 +0100 (Wed, 30 Jan 2019) | 31 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_long.m
M       cat_conf_long.m
M       cat_conf_tools.m
M       cat_long_main.m
M       cat_long_multi_run.m
D       cat_vol_average.m
        > moved to development/cat_vol_average.m
A       cat_vol_avg.m
M       cat_vol_groupwise_ls.m
M       cat_vol_headtrimming.m
M       cat_vol_series_align.m
A  +    development/cat_vol_average.m
        > moved from cat_vol_average.m

(1) Changed: Moved unused cat_vol_average.m to developer folder.
(2) Changed: Added option to reduce bounding box at final resolution level in
    longitudinal registration.
(3) Added: Created new tool for calculating average of up to 5D data of same
    dimension and voxel size.
(4) Changed: Noise estimate in longitudinal tool is not used anymore because of
    instabilities for data from different scanners.
(5) Fixed: Use of Hessian matrix in longitudinal registration only if finite.
(6) Changed: Removed warp option for longitudinal pipeline because average
    deformation field will be now always written.
(7) Changed: Updated longitudinal pipeline w.r.t. to the actual changes. The
    spatial registration is now estimated from the mean deformation field of
    all subjects instead of the deformation field of the mean image. This will
    be more stable for larger changes between the time points.

------------------------------------------------------------------------
r1423 | gaser | 2019-01-29 07:54:54 +0100 (Tue, 29 Jan 2019) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_long.m
M       cat_conf_tools.m
M       cat_long_multi_run.m
M       cat_vol_groupwise_ls.m
M       cat_vol_series_align.m
M       html/cat.html

(1) Fixed: Use of brainmask for rigid registration is now fixed.
(2) Changed: Added option for writing deformations in longitudinal tool.

------------------------------------------------------------------------
r1422 | gaser | 2019-01-21 23:39:21 +0100 (Mon, 21 Jan 2019) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_vol_groupwise_ls.m
M       cat_vol_series_align.m

Chamged: Extended longitudinal rigid registration by non-linear registration.

------------------------------------------------------------------------
r1421 | gaser | 2019-01-18 16:41:16 +0100 (Fri, 18 Jan 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_main_reportfig.m

Changed: Switched off some warnings in cat_main_reportfig.m for windows systems.

------------------------------------------------------------------------
r1420 | gaser | 2019-01-18 16:37:58 +0100 (Fri, 18 Jan 2019) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main_reportfig.m
M       html/cat.html

Changed: Switched off some warnings in cat_main_reportfig.m for windows systems.

------------------------------------------------------------------------
r1419 | gaser | 2019-01-18 16:06:47 +0100 (Fri, 18 Jan 2019) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_long.m
M       cat_batch_long.sh
M       cat_long_main.m
M       cat_long_multi_run.m
M       cat_vol_groupwise_ls.m
M       tbx_cfg_cat.m

(1) Changed: Updated longitudinal pipeline and skipped use of trimmed images.
(2) Changed: Hided experimental batch options for older pipelines.
(3) Changed: Updated cat_vol_groupwise_ls.m w.r.t. last SPM12 update.
(4) Changed: For rigid longitudinal registration is now the median instead of
    the avg estimated and used from all time points to consider larger changes
    between the time points.
(5) Fixed: Removed bug in shell script for longitudinal pipeline that ignored
    surface flag.

------------------------------------------------------------------------
r1418 | dahnke | 2019-01-18 15:10:04 +0100 (Fri, 18 Jan 2019) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_run.m

1) Changed:  Modified registration menu.

------------------------------------------------------------------------
r1417 | dahnke | 2019-01-18 10:25:15 +0100 (Fri, 18 Jan 2019) | 17 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_long_main.m
M       cat_main.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_stat_marks.m
M       cat_surf_createCS.m
M       cat_vol_groupwise_ls.m
M       cat_vol_qa.m
M       html/cat.html

1) Fixed:   Corrected small bugs in cat_main_report.
2) New:     Added rating for topological defects and defect area to
            create colorized output in the cat report (only experts).

------------------------------------------------------------------------
r1416 | gaser | 2019-01-16 15:57:25 +0100 (Wed, 16 Jan 2019) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_long_main.m
M       cat_main_reportfig.m
MM      cat_surf_create_TPM_hull_surface.m
M       cat_vol_groupwise_ls.m
M       html/cat.html
 M      templates_surfaces/bh.headbrain.TPM.gii

(1) Changed: Updated longitudinal pipeline to use trimmed images based on
    bounding box of average T1 image.
(2) Changed: Suppress some warning for windows systems.
(3) Changed: Updated cat_vol_groupwise_ls.m w.r.t. last SPM12 update.

------------------------------------------------------------------------
r1415 | gaser | 2019-01-14 15:20:53 +0100 (Mon, 14 Jan 2019) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_main_reportfig.m
M       cat_run_job1070.m
M       cat_surf_createCS.m

Fixed: Corrected some warnings on older Matlab versions.

------------------------------------------------------------------------
r1414 | dahnke | 2019-01-14 09:16:00 +0100 (Mon, 14 Jan 2019) | 26 lines

Changed paths:
M       CHANGES.txt
M       cat_io_colormaps.m
M       cat_io_report.m
M       cat_main.m
M       cat_main_amap.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m
M       cat_run_job.m
M       cat_run_job_APP_init1070.m
M       cat_run_job_APRGs.m
M       cat_run_newcatch.m
M       cat_surf_createCS.m
A       cat_surf_create_TPM_hull_surface.m
M       cat_surf_render2.m
A       templates_surfaces/bh.headbrain.TPM.gii

1) Fixed:   Updated segmentation output in error report and preprocessing functions.
2) Fixed:   Corrected problems with the background segmentation in cat_run_job_APP1070.
3) Fixed:   Try to optimize the affine registration by changes in cat_run_job_APRGs!
4) Fixed:   Revert last changes in cat_surf_createCS because of errors!
5) New:     Added TPM brain and head surface creation script for (error) report overlay.
6) New:     Added rigid transformation for report surface output.


------------------------------------------------------------------------
r1413 | gaser | 2019-01-11 12:18:03 +0100 (Fri, 11 Jan 2019) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_results.m
M       html/cat.html

Changed: cat_surf_results.m is now using just one window.

------------------------------------------------------------------------
r1412 | dahnke | 2019-01-09 09:56:17 +0100 (Wed, 09 Jan 2019) | 25 lines

Changed paths:
M       CHANGES.txt
M       cat_io_colormaps.m
M       cat_io_report.m
M       cat_main.m
M       cat_main_registration2.m
M       cat_main_reportfig.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job_APP_SPMinit.m
M       cat_vol_partvol.m
M       compile.m

1) Fixed:   Corrected bugs in chimpanzee pipeline.
2) Fixed:   Corrected bugs in template setings in cat_run_job.
3) Fixed:   Corrected bugs in error report creation.
4) Fixed:   Modified APP test function in cat_run_job.
5) Changed: Updated cat_report segmentation output.
6) Changed: Updated cat_main_reportfig and related parts in cat_main.
            Replaced the brain segmentation output of the p0 by a more
7) Fixed:   Corrected blood vessel detection problems in cat_vol_partvol.
8) New:     Added some colormaps in cat_io_colormaps and another
            sulcus case (manual use) in compile.


------------------------------------------------------------------------
r1411 | gaser | 2019-01-08 10:19:59 +0100 (Tue, 08 Jan 2019) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m

Changed: Changed initialization of some variables to prevent warnings for
writing int32 gifti files.

------------------------------------------------------------------------
r1410 | gaser | 2019-01-04 17:19:35 +0100 (Fri, 04 Jan 2019) | 19 lines

Changed paths:
A  +    CAT12-Manual-Word-Old.docx
        > moved from CAT12-Manual.docx
D       CAT12-Manual.docx
        > moved to CAT12-Manual-Word-Old.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_long_main.m
M       cat_surf_results.m
M       html/cat.html

(1) Fixed: Masking in longitudinal batch was not correctly set.
(2) Changed: Switched to Google Docs for manual (bye bye Microsoft!).
(3) Fixed: Corrected many bugs in cat_surf_results.m for plotting function
    and recognition of 32k meshes.
(4) Changed: Added option to plot raw data in cat_surf_results.m.
(5) Changed: Updated CAT12 manual.

------------------------------------------------------------------------
r1409 | gaser | 2018-12-21 15:41:26 +0100 (Fri, 21 Dec 2018) | 7 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt

Changed: Updated CAT12 manual.

------------------------------------------------------------------------
r1408 | gaser | 2018-12-20 16:05:05 +0100 (Thu, 20 Dec 2018) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_run_job.m
M       cat_surf_results.m
M       html/cat.html

Fixed: Data display was not working for Displaying surface results if analysis
folder was moved.


------------------------------------------------------------------------
r1407 | dahnke | 2018-12-15 20:58:05 +0100 (Sat, 15 Dec 2018) | 20 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_kamap.m
M       cat_main_registration.m
M       cat_main_registration2.m
M       cat_run_job.m
M       cat_run_job_APP_init.m
M       cat_run_job_APP_init1070.m

(1) Changed:    Updated handling of cat_main_clean_gwc in cat_main.
                Removed uncomment code of old LAS call.
(2) Fixed:      Corrected bugs in cat_main_kamap.
(3) Fixed:      Corrected bug of affine handling in cat_main_registration(2).
(4) New:        Added try-catch block for APP preprocessing with simple test
                and backup routine in case of errors including visual warning.
(5) Fixed:      Corrected problems with high intensity background (MP2RAGE) in
                cat_run_job_APP_init(1070).


------------------------------------------------------------------------
r1406 | gaser | 2018-12-13 23:36:31 +0100 (Thu, 13 Dec 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_plot_boxplot.m

Fixed: Solved issues with boxplot tool and TickLabelInterpreter.

------------------------------------------------------------------------
r1405 | gaser | 2018-12-13 22:45:37 +0100 (Thu, 13 Dec 2018) | 155 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
!       check_pipeline
!       check_pipeline/IXI002-Guys-0828-T1.nii
!       check_pipeline/analysis
!       check_pipeline/analysis/surface
!       check_pipeline/analysis/surface/RPV.dat
!       check_pipeline/analysis/surface/RPV.gii
!       check_pipeline/analysis/surface/SPM.mat
!       check_pipeline/analysis/surface/spmF_0001.dat
!       check_pipeline/analysis/surface/spmF_0001.gii
!       check_pipeline/analysis/surface/spmT_0002.dat
!       check_pipeline/analysis/surface/spmT_0002.gii
!       check_pipeline/analysis/volume
!       check_pipeline/analysis/volume/RPV.nii
!       check_pipeline/analysis/volume/SPM.mat
!       check_pipeline/analysis/volume/spmF_0001.nii
!       check_pipeline/analysis/volume/spmT_0002.nii
!       check_pipeline/batch_surface_pipeline.m
!       check_pipeline/batch_volume_pipeline.m
!       check_pipeline/label_orig
!       check_pipeline/label_orig/catROI_IXI002-Guys-0828-T1.mat
!       check_pipeline/label_orig/catROI_IXI002-Guys-0828-T1.xml
!       check_pipeline/label_orig/catROI_IXI016-Guys-0697-T1.mat
!       check_pipeline/label_orig/catROI_IXI016-Guys-0697-T1.xml
!       check_pipeline/label_orig/catROI_IXI017-Guys-0698-T1.mat
!       check_pipeline/label_orig/catROI_IXI017-Guys-0698-T1.xml
!       check_pipeline/label_orig/catROI_IXI019-Guys-0702-T1.mat
!       check_pipeline/label_orig/catROI_IXI019-Guys-0702-T1.xml
!       check_pipeline/label_orig/catROI_IXI020-Guys-0700-T1.mat
!       check_pipeline/label_orig/catROI_IXI020-Guys-0700-T1.xml
!       check_pipeline/label_orig/catROI_IXI021-Guys-0703-T1.mat
!       check_pipeline/label_orig/catROI_IXI021-Guys-0703-T1.xml
!       check_pipeline/label_orig/catROI_IXI022-Guys-0701-T1.mat
!       check_pipeline/label_orig/catROI_IXI022-Guys-0701-T1.xml
!       check_pipeline/label_orig/catROI_IXI023-Guys-0699-T1.mat
!       check_pipeline/label_orig/catROI_IXI023-Guys-0699-T1.xml
!       check_pipeline/label_orig/catROI_IXI024-Guys-0705-T1.mat
!       check_pipeline/label_orig/catROI_IXI024-Guys-0705-T1.xml
!       check_pipeline/label_orig/catROI_IXI025-Guys-0852-T1.mat
!       check_pipeline/label_orig/catROI_IXI025-Guys-0852-T1.xml
!       check_pipeline/label_orig/catROI_IXI026-Guys-0696-T1.mat
!       check_pipeline/label_orig/catROI_IXI026-Guys-0696-T1.xml
!       check_pipeline/label_orig/catROI_IXI027-Guys-0710-T1.mat
!       check_pipeline/label_orig/catROI_IXI027-Guys-0710-T1.xml
!       check_pipeline/label_orig/catROI_IXI028-Guys-1038-T1.mat
!       check_pipeline/label_orig/catROI_IXI028-Guys-1038-T1.xml
!       check_pipeline/label_orig/catROI_IXI029-Guys-0829-T1.mat
!       check_pipeline/label_orig/catROI_IXI029-Guys-0829-T1.xml
!       check_pipeline/label_orig/catROI_IXI030-Guys-0708-T1.mat
!       check_pipeline/label_orig/catROI_IXI030-Guys-0708-T1.xml
!       check_pipeline/label_orig/catROI_IXI031-Guys-0797-T1.mat
!       check_pipeline/label_orig/catROI_IXI031-Guys-0797-T1.xml
!       check_pipeline/label_orig/catROI_IXI036-Guys-0736-T1.mat
!       check_pipeline/label_orig/catROI_IXI036-Guys-0736-T1.xml
!       check_pipeline/label_orig/catROI_IXI037-Guys-0704-T1.mat
!       check_pipeline/label_orig/catROI_IXI037-Guys-0704-T1.xml
!       check_pipeline/label_orig/catROI_IXI038-Guys-0729-T1.mat
!       check_pipeline/label_orig/catROI_IXI038-Guys-0729-T1.xml
!       check_pipeline/label_orig/catROI_IXI040-Guys-0724-T1.mat
!       check_pipeline/label_orig/catROI_IXI040-Guys-0724-T1.xml
!       check_pipeline/label_orig/catROIs_IXI002-Guys-0828-T1.mat
!       check_pipeline/label_orig/catROIs_IXI002-Guys-0828-T1.xml
!       check_pipeline/label_orig/catROIs_IXI016-Guys-0697-T1.mat
!       check_pipeline/label_orig/catROIs_IXI016-Guys-0697-T1.xml
!       check_pipeline/label_orig/catROIs_IXI017-Guys-0698-T1.mat
!       check_pipeline/label_orig/catROIs_IXI017-Guys-0698-T1.xml
!       check_pipeline/label_orig/catROIs_IXI019-Guys-0702-T1.mat
!       check_pipeline/label_orig/catROIs_IXI019-Guys-0702-T1.xml
!       check_pipeline/label_orig/catROIs_IXI020-Guys-0700-T1.mat
!       check_pipeline/label_orig/catROIs_IXI020-Guys-0700-T1.xml
!       check_pipeline/label_orig/catROIs_IXI021-Guys-0703-T1.mat
!       check_pipeline/label_orig/catROIs_IXI021-Guys-0703-T1.xml
!       check_pipeline/label_orig/catROIs_IXI022-Guys-0701-T1.mat
!       check_pipeline/label_orig/catROIs_IXI022-Guys-0701-T1.xml
!       check_pipeline/label_orig/catROIs_IXI023-Guys-0699-T1.mat
!       check_pipeline/label_orig/catROIs_IXI023-Guys-0699-T1.xml
!       check_pipeline/label_orig/catROIs_IXI024-Guys-0705-T1.mat
!       check_pipeline/label_orig/catROIs_IXI024-Guys-0705-T1.xml
!       check_pipeline/label_orig/catROIs_IXI025-Guys-0852-T1.mat
!       check_pipeline/label_orig/catROIs_IXI025-Guys-0852-T1.xml
!       check_pipeline/label_orig/catROIs_IXI026-Guys-0696-T1.mat
!       check_pipeline/label_orig/catROIs_IXI026-Guys-0696-T1.xml
!       check_pipeline/label_orig/catROIs_IXI027-Guys-0710-T1.mat
!       check_pipeline/label_orig/catROIs_IXI027-Guys-0710-T1.xml
!       check_pipeline/label_orig/catROIs_IXI028-Guys-1038-T1.mat
!       check_pipeline/label_orig/catROIs_IXI028-Guys-1038-T1.xml
!       check_pipeline/label_orig/catROIs_IXI029-Guys-0829-T1.mat
!       check_pipeline/label_orig/catROIs_IXI029-Guys-0829-T1.xml
!       check_pipeline/label_orig/catROIs_IXI030-Guys-0708-T1.mat
!       check_pipeline/label_orig/catROIs_IXI030-Guys-0708-T1.xml
!       check_pipeline/label_orig/catROIs_IXI031-Guys-0797-T1.mat
!       check_pipeline/label_orig/catROIs_IXI031-Guys-0797-T1.xml
!       check_pipeline/label_orig/catROIs_IXI036-Guys-0736-T1.mat
!       check_pipeline/label_orig/catROIs_IXI036-Guys-0736-T1.xml
!       check_pipeline/label_orig/catROIs_IXI037-Guys-0704-T1.mat
!       check_pipeline/label_orig/catROIs_IXI037-Guys-0704-T1.xml
!       check_pipeline/label_orig/catROIs_IXI038-Guys-0729-T1.mat
!       check_pipeline/label_orig/catROIs_IXI038-Guys-0729-T1.xml
!       check_pipeline/label_orig/catROIs_IXI040-Guys-0724-T1.mat
!       check_pipeline/label_orig/catROIs_IXI040-Guys-0724-T1.xml
!       check_pipeline/mri
!       check_pipeline/mri/mwp1IXI002-Guys-0828-T1.nii
!       check_pipeline/mri/mwp1IXI016-Guys-0697-T1.nii
!       check_pipeline/mri/mwp1IXI017-Guys-0698-T1.nii
!       check_pipeline/mri/mwp1IXI019-Guys-0702-T1.nii
!       check_pipeline/report
!       check_pipeline/report/cat_IXI002-Guys-0828-T1.mat
!       check_pipeline/report/cat_IXI002-Guys-0828-T1.xml
!       check_pipeline/report/cat_IXI016-Guys-0697-T1.mat
!       check_pipeline/report/cat_IXI016-Guys-0697-T1.xml
!       check_pipeline/report/cat_IXI017-Guys-0698-T1.mat
!       check_pipeline/report/cat_IXI017-Guys-0698-T1.xml
!       check_pipeline/report/cat_IXI019-Guys-0702-T1.mat
!       check_pipeline/report/cat_IXI019-Guys-0702-T1.xml
!       check_pipeline/surf
!       check_pipeline/surf/lh.central.IXI002-Guys-0828-T1.gii
!       check_pipeline/surf/lh.central.IXI016-Guys-0697-T1.gii
!       check_pipeline/surf/lh.central.IXI017-Guys-0698-T1.gii
!       check_pipeline/surf/lh.central.IXI019-Guys-0702-T1.gii
!       check_pipeline/surf/lh.sphere.IXI002-Guys-0828-T1.gii
!       check_pipeline/surf/lh.sphere.IXI016-Guys-0697-T1.gii
!       check_pipeline/surf/lh.sphere.IXI017-Guys-0698-T1.gii
!       check_pipeline/surf/lh.sphere.IXI019-Guys-0702-T1.gii
!       check_pipeline/surf/lh.sphere.reg.IXI002-Guys-0828-T1.gii
!       check_pipeline/surf/lh.sphere.reg.IXI016-Guys-0697-T1.gii
!       check_pipeline/surf/lh.sphere.reg.IXI017-Guys-0698-T1.gii
!       check_pipeline/surf/lh.sphere.reg.IXI019-Guys-0702-T1.gii
!       check_pipeline/surf/lh.thickness.IXI002-Guys-0828-T1
!       check_pipeline/surf/lh.thickness.IXI016-Guys-0697-T1
!       check_pipeline/surf/lh.thickness.IXI017-Guys-0698-T1
!       check_pipeline/surf/lh.thickness.IXI019-Guys-0702-T1
!       check_pipeline/surf/rh.central.IXI002-Guys-0828-T1.gii
!       check_pipeline/surf/rh.central.IXI016-Guys-0697-T1.gii
!       check_pipeline/surf/rh.central.IXI017-Guys-0698-T1.gii
!       check_pipeline/surf/rh.central.IXI019-Guys-0702-T1.gii
!       check_pipeline/surf/rh.sphere.IXI002-Guys-0828-T1.gii
!       check_pipeline/surf/rh.sphere.IXI016-Guys-0697-T1.gii
!       check_pipeline/surf/rh.sphere.IXI017-Guys-0698-T1.gii
!       check_pipeline/surf/rh.sphere.IXI019-Guys-0702-T1.gii
!       check_pipeline/surf/rh.sphere.reg.IXI002-Guys-0828-T1.gii
!       check_pipeline/surf/rh.sphere.reg.IXI016-Guys-0697-T1.gii
!       check_pipeline/surf/rh.sphere.reg.IXI017-Guys-0698-T1.gii
!       check_pipeline/surf/rh.sphere.reg.IXI019-Guys-0702-T1.gii
!       check_pipeline/surf/rh.thickness.IXI002-Guys-0828-T1
!       check_pipeline/surf/rh.thickness.IXI016-Guys-0697-T1
!       check_pipeline/surf/rh.thickness.IXI017-Guys-0698-T1
!       check_pipeline/surf/rh.thickness.IXI019-Guys-0702-T1
M       html/cat_orthogonality.html

Changed: Updated information about design orthogonality in online help
and manual.

------------------------------------------------------------------------
r1404 | gaser | 2018-12-13 13:58:05 +0100 (Thu, 13 Dec 2018) | 23 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_conf_long.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_long_main.m
M       cat_main_APRG.m
M       cat_run_job.m
MM      cat_run_job_APRGs.m
M       cat_vol_headtrimming.m
M       html/cat.html
M       html/cat_orthogonality.html

(1) Changed: Added masking option to data-trimming function.
(2) Changed: Slightly changed value for detection of skull-stripped data.
(3) Changed: Added data-trimming step to longitudinal pipeline to speed-up
    processing of time points.
(4) Changed: Updated cutting threshold for APRG approach based on validation
    data.
(5) Changed: Updated help text.

------------------------------------------------------------------------
r1403 | dahnke | 2018-12-05 20:29:11 +0100 (Wed, 05 Dec 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_main_kamap.m

(1) Changed:    Update kamap preprocessing.

------------------------------------------------------------------------
r1402 | dahnke | 2018-12-05 17:11:48 +0100 (Wed, 05 Dec 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m

(1) Fixed:  Corrected bug in batch mode of the trimming tool.

------------------------------------------------------------------------
r1401 | dahnke | 2018-12-04 23:36:50 +0100 (Tue, 04 Dec 2018) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat_io_report.m
M       cat_main.m
M       cat_main_clean_gwc.m
M       cat_main_kamap.m
M       cat_main_reportfig.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m

(1) Changed:   	Include brain limitation in cat_main_clean_gwc for speedup
                and removed limitations in cat_main and cat_main_updateSPM.
(2) New:        Added harder removal of meninges by morphological operations
                close to the skull in cat_main_clean_gwc.
(3) Fixed:      Corrected bugs in cat_io_report.
(4) Changed:    Activate rewritten LAS routine in cat_main.
(5) Changed:    Updated cat_main_kamap cleanup calls.


------------------------------------------------------------------------
r1400 | gaser | 2018-12-03 17:06:50 +0100 (Mon, 03 Dec 2018) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
MM      batches/cattest/cat12_105_MAIN_segment_1173plus.m
MM      batches/cattest/cat12_106_MAIN_segment_1173.m
M       cat_main_APRG.m
M       html/cat.html
M       html/cat_starting.html

(1) Changed: Updated threshold for APRG skull-stripping to include slightly
    less CSF.
(2) Changed: Updated order of surface TFCE in Quick Starting Guide.

------------------------------------------------------------------------
r1399 | dahnke | 2018-12-01 22:30:42 +0100 (Sat, 01 Dec 2018) | 28 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_APRG.m
M       cat_main_cleanup.m
M       cat_main_gintnormi.m
M       cat_main_reportfig.m
M       cat_run_job.m
M       cat_run_job_APP_init.m
M       cat_run_job_APP_init1070.m
M       cat_run_job_APRGs.m

(1) Fixed:   	Corrected WM threshold problems in cat_run_job_APPinit*
		preprocessing routines with high GM-WM contrast.
(2) New:	Added kmeans-based intensity normalization routine in APP
		preprocessings to reduce problems in images with ultrahigh
		GM-WM contrast (eg. INDI_OUL).
(3) Fixed:   	Corrected bug in cat_run_job_APRGs (missed to mask the brain
		for spm_maff8).
(4) Fixed: 	Corrected small bugs in the intensity normalization of
		cat_run_job_APRGs.
(5) Documented:	Added example for general call of cat_main_gintnormi for
		intensity normalization.
(6) Fixed:	Corrected undesired SPM graphics figure popup of CAT report
		in parallel processing.
(7) Changed:	Reduced cleanup in cerebral areas close to the cerebrum.


------------------------------------------------------------------------
r1398 | dahnke | 2018-11-29 18:13:22 +0100 (Thu, 29 Nov 2018) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_LAS.m
M       cat_main_registration.m
M       cat_main_reportstr.m
M       cat_main_updateSPM.m
M       cat_run_job.m
A       cat_run_job_APRGs.m
M       cat_vol_grad.m
M       cat_vol_partvol.m

(1) Fixed:    Corrected bugs in older Matlab versions in cat_main,
							cat_main_reportstr, cat_vol_partvol, cat_main_updateSPM.
(2) New:      Added affine GM registration in cat_main_registration
              to improve the Dartel/Shooting initialization.
(3) New:	  	Added skull-stripping affine registration routine
							cat_run_job_APRGs in cat_run_job (alpha status!).

------------------------------------------------------------------------
r1397 | gaser | 2018-11-29 13:57:07 +0100 (Thu, 29 Nov 2018) | 20 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_batch_cat.m
M       cat_conf_opts.m
M       cat_defaults.m
M       cat_run.m
M       cat_run1173/cat_surf_createCS1173.m
M       html/cat.html
M       html/cat_methods_RBM.html
M       spm_cat12.m

(1) Changed: Version information.
(2) Fixed: Corrected wrong name of T1 template in html pages.
(3) Fixed: Corrected call to CAT_DeformSurf to consider additional parameter.
(4) Fixed: Typos
(5) Fixed: Updated deletion of fields in cat_batch_cat.m
(6) Changed: Updated Makefile according to additional cat versions.

------------------------------------------------------------------------
r1396 | dahnke | 2018-11-28 12:37:23 +0100 (Wed, 28 Nov 2018) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_opts.m
M       cat_defaults.m
M       cat_run.m

(1) New:    Added SPM accuracy parameter in GUI and cat_defaults.

------------------------------------------------------------------------
r1395 | dahnke | 2018-11-21 16:25:23 +0100 (Wed, 21 Nov 2018) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_cleanup.m
M       cat_surf_createCS.m
M       cat_surf_render2.m

(1) Fixed:     Modified cat_main_cleanup routine to avoid local cuts into the brain.

------------------------------------------------------------------------
r1394 | dahnke | 2018-11-20 10:19:37 +0100 (Tue, 20 Nov 2018) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_main_kamap.m
M       cat_main_registration.m
M       cat_surf_createCS.m

(1) Changed:    Worked on problems in the kamap pipeline.
(2) Fixed:      Corrected bug in Shooting call due to SPM update.
(3) Fixed:      Suppressed MATLAB:subscripting:noSubscriptsSpecified
                warning created in GIFTI output routine (gifti/subsref:45).

------------------------------------------------------------------------
r1393 | dahnke | 2018-11-19 09:36:43 +0100 (Mon, 19 Nov 2018) | 20 lines

Changed paths:
M       CHANGES.txt
M       batches/cattest/cat12_101_MAIN_segment.m
A       batches/cattest/cat12_105_MAIN_segment_1173plus.m
A       batches/cattest/cat12_106_MAIN_segment_1173.m
M       batches/cattest/cat12_308_SBM_Surf2ROI.m
M       cat_conf_opts.m
M       cat_main.m
M       cat_main_kamap.m
M       cat_main_registration.m
M       cat_main_updateWMHs.m
M       cat_run1173plus/cat_conf_extopts1173plus.m
M       cat_run1173plus/cat_run_job1173plus.m
M       cat_tst_cattest.m
M       tbx_cfg_cat.m

(1) Fixed:   Corrected small bugs in cat_main and batch generation.
(2) Fixed:   Updated cat_tst_cattest and batches for current cat version.


------------------------------------------------------------------------
r1392 | gaser | 2018-11-15 21:24:07 +0100 (Thu, 15 Nov 2018) | 25 lines

Changed paths:
M       CAT12-Manual.docx
M       CHANGES.txt
M       cat_conf_tools.m
MM      cat_main_APRG.m
MM      cat_main_kamap.m
MM      cat_run1173plus/cat_conf_extopts1173plus.m
MM      cat_run1173plus/cat_conf_long1173plus.m
MM      cat_run1173plus/cat_conf_opts1173plus.m
MM      cat_run1173plus/cat_defaults1173plus.m
MM      cat_run1173plus/cat_get_defaults1173plus.m
MM      cat_run1173plus/cat_main1173plus.m
MM      cat_run1173plus/cat_run1173plus.m
MM      cat_run1173plus/cat_run_job10701173plus.m
MM      cat_run1173plus/cat_run_job1173plus.m
MM      cat_run1173plus/cat_run_newcatch1173plus.m
M       cat_stat_spm2x.m

(1) Fixed: Removed option to convert T-maps to Cohen's d map, because the
    applied equation was not correct and there seem to be no general
    conversion possible for a GLM. Thanks to Alessandro Meani for pointing
    to that issue.
(2) Fixed: Updated equations for converting T-maps to correlation coefficient
    and from F-maps to R squared.

------------------------------------------------------------------------
r1391 | dahnke | 2018-11-12 22:30:23 +0100 (Mon, 12 Nov 2018) | 20 lines

Changed paths:
M       CHANGES.txt
M       batches/cattest/cat12_101_MAIN_segment.m
M       cat_defaults.m
M       cat_main_updateSPM.m
M       cat_run1173/cat_main1173.m
M       cat_run1173/cat_run_job10701173.m
M       cat_run1173/cat_run_job1173.m
M       cat_run1173/cat_run_newcatch1173.m
M       cat_run1173plus/cat_main1173plus.m
M       cat_run1173plus/cat_run_job10701173plus.m
M       cat_run1173plus/cat_run_job1173plus.m
M       cat_run1173plus/cat_run_newcatch1173plus.m
M       cat_run_newcatch.m
M       cat_tst_cattest.m

(1) Fixed:   Corrected many small bugs (missing variable) in cat_main_updataSPM.
(2) Fixed:   Also copy catlog_*.txt into error directory (cat_run_newcatch*).


------------------------------------------------------------------------
r1390 | dahnke | 2018-11-12 09:44:38 +0100 (Mon, 12 Nov 2018) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_run1173/cat_run1173.m
M       cat_run1173plus/cat_conf_extopts1173plus.m
M       cat_run1173plus/cat_run1173plus.m
M       cat_surf_createCS.m

(1) Fixed:      Corrected bugs in cat_main_createCS and cat_run1173plus.

------------------------------------------------------------------------
r1389 | dahnke | 2018-11-11 11:39:41 +0100 (Sun, 11 Nov 2018) | 57 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
A       cat_main_APRG.m
MM      cat_main_amap.m
 M      cat_main_clean_gwc.m
A       cat_main_kamap.m
MM      cat_main_reportcmd.m
MM      cat_main_reportfig.m
MM      cat_main_reportstr.m
MM      cat_main_roi.m
MM      cat_main_updateSPM.m
MM      cat_main_updateWMHs.m
MM      cat_main_write.m
MM      cat_run1173/cat_conf_ROI1173.m
MM      cat_run1173/cat_conf_extopts1173.m
MM      cat_run1173/cat_conf_long1173.m
MM      cat_run1173/cat_conf_opts1173.m
MM      cat_run1173/cat_defaults1173.m
MM      cat_run1173/cat_get_defaults1173.m
MM      cat_run1173/cat_long_main1173.m
MM      cat_run1173/cat_long_multi_run1173.m
MM      cat_run1173/cat_main1173.m
MM      cat_run1173/cat_main_LAS1173.m
MM      cat_run1173/cat_main_gcut1173.m
MM      cat_run1173/cat_main_registration1173.m
MM      cat_run1173/cat_run1173.m
MM      cat_run1173/cat_run_job10701173.m
MM      cat_run1173/cat_run_job1173.m
MM      cat_run1173/cat_run_job_APP_SPM1173.m
MM      cat_run1173/cat_run_job_APP_final.m
MM      cat_run1173/cat_run_job_APP_init10701173.m
MM      cat_run1173/cat_run_newcatch1173.m
MM      cat_run1173/cat_surf_createCS1173.m
MM      cat_run1173/cat_tst_qa1173.m
MM      cat_run1173/cat_vol_isarnlm.m
MM      cat_run1173/cat_vol_partvol1173.m
MM      cat_run1173/cat_vol_sanlm1173.m
A       cat_run1173plus
A       cat_run1173plus/cat_conf_extopts1173plus.m
A       cat_run1173plus/cat_conf_long1173plus.m
A       cat_run1173plus/cat_conf_opts1173plus.m
A       cat_run1173plus/cat_defaults1173plus.m
A       cat_run1173plus/cat_get_defaults1173plus.m
A       cat_run1173plus/cat_main1173plus.m
A       cat_run1173plus/cat_run1173plus.m
A       cat_run1173plus/cat_run_job10701173plus.m
A       cat_run1173plus/cat_run_job1173plus.m
A       cat_run1173plus/cat_run_newcatch1173plus.m
MM      cat_spm_preproc8.m
M       tbx_cfg_cat.m

(1) New:        Added 1173plus segmentation.
(2) Changed:    Further cleanup of cat_main.
(3) Changed:    Separated new skull-stripping.


------------------------------------------------------------------------
r1388 | dahnke | 2018-11-06 16:29:48 +0100 (Tue, 06 Nov 2018) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_roi.m
A       cat_main_updateSPM.m
A       cat_main_updateWMHs.m
A       cat_main_write.m

(1) Changed:    Moved CAT NIFTI output from cat_main to cat_main_write.
(2) Changed:    Moved WMH correction functions from cat_main to
                cat_main_updateWMHs and cat_main_fillWMHs.


------------------------------------------------------------------------
r1387 | dahnke | 2018-11-06 13:59:32 +0100 (Tue, 06 Nov 2018) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_opts.m
M       cat_main.m
A       cat_main_reportcmd.m
A       cat_main_reportfig.m
A       cat_main_reportstr.m
A       cat_main_roi.m

(1) Changed:    Separated CAT report creation from cat_main as
                cat_main_reportstr, cat_main_reportfig and cat_main_reportcmd.
(2) Changed:    Separated CAT ROI functions from cat_main as cat_main_roi.



------------------------------------------------------------------------
r1386 | dahnke | 2018-11-05 16:15:06 +0100 (Mon, 05 Nov 2018) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
A       cat_main_amap.m
A       cat_main_clean_gwc.m
M       cat_run1173/cat_main1173.m
A       cat_run1173/cat_surf_createCS1173.m
M       cat_surf_createCS.m
M       cat_vol_morph.m

(1) Changed:    Separated initial k-means AMAP segmentation from cat_main as
                cat_main_amap and added documentation. No behavioral changes.
(2) Changed:    Separated clean-up function from cat_main as cat_main_clean_gwc.
                No behavioral changes.


------------------------------------------------------------------------
r1385 | dahnke | 2018-11-02 18:05:12 +0100 (Fri, 02 Nov 2018) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_run_job_APP_SPMinit.m
M       cat_vol_sanlm.m

(1) Fixed:  Fixed "Cannot read header extension." error in cat_vol_sanlm.
(2) Fixed:  Corrected bug in cat_run_job_SPMinit.

------------------------------------------------------------------------
r1384 | dahnke | 2018-10-31 20:55:27 +0100 (Wed, 31 Oct 2018) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_gintnorm.m
M       cat_run1173/cat_main1173.m
M       cat_run_job.m
M       cat_run_job_APP_SPMfinal.m
M       cat_run_job_APP_SPMinit.m
M       cat_vol_imcalc.m

(1) Fixed:  Corrected bugs in cat_conf_opts, cat_run1173 and cat_main1173.
(2) Fixed:  Corrected interpolation bug "Cannot read header extension.{U+201C} in
            cat_run_job_APP_SPM* and cat_run_job.
(3) Fixed:  Corrected type convertation in cat_vol_imcalc.
(4) Fixed:  Added skull-stripped handling in cat_run_job_APP_SPMinit and
            cat_run_job_APPfinal and cat_main_gintnorm.



------------------------------------------------------------------------
r1383 | dahnke | 2018-10-29 07:07:56 +0100 (Mon, 29 Oct 2018) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_opts.m
M       cat_run1173/cat_run1173.m
MM      cat_run_job_APP_SPMinit.m
 M      html/icons/status_failed.old.png

(1) Fixed:  Corrected bugs in cat_conf_opts and cat_run1173.


------------------------------------------------------------------------
r1382 | dahnke | 2018-10-26 22:28:41 +0200 (Fri, 26 Oct 2018) | 33 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_opts.m
A       cat_run1173
A       cat_run1173/cat_conf_ROI1173.m
A       cat_run1173/cat_conf_extopts1173.m
A       cat_run1173/cat_conf_long1173.m
A       cat_run1173/cat_conf_opts1173.m
A       cat_run1173/cat_defaults1173.m
A       cat_run1173/cat_get_defaults1173.m
A       cat_run1173/cat_long_main1173.m
A       cat_run1173/cat_long_multi_run1173.m
A       cat_run1173/cat_main1173.m
A       cat_run1173/cat_main_LAS1173.m
A       cat_run1173/cat_main_gcut1173.m
A       cat_run1173/cat_main_registration1173.m
A       cat_run1173/cat_run1173.m
A       cat_run1173/cat_run_job10701173.m
A       cat_run1173/cat_run_job1173.m
A       cat_run1173/cat_run_job_APP_SPM1173.m
A       cat_run1173/cat_run_job_APP_final.m
A       cat_run1173/cat_run_job_APP_init10701173.m
A       cat_run1173/cat_run_newcatch1173.m
A       cat_run1173/cat_tst_qa1173.m
A       cat_run1173/cat_vol_isarnlm.m
A       cat_run1173/cat_vol_partvol1173.m
A       cat_run1173/cat_vol_sanlm1173.m
M       cat_run_job.m
M       tbx_cfg_cat.m

(1) New:    Added old preprocessing pipeline 1173 and related functions.
(2) Fixed:  Corrected small bugs in cat_conf_opts und cat_run_job.

------------------------------------------------------------------------
r1381 | dahnke | 2018-10-25 17:24:14 +0200 (Thu, 25 Oct 2018) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_run_job.m
A       html/icons/status_failed.old.png

(1) Fixed:      Corrected PD/T2 skull-stripping error.
(2) Fixed:      Corrected background error in skull-stripped data.
(3) Fixed:      Updated output of cat_report.

------------------------------------------------------------------------
r1380 | dahnke | 2018-10-24 17:15:09 +0200 (Wed, 24 Oct 2018) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main.m
M       cat_main_registration.m
M       cat_main_registration2.m
M       cat_run_job.m

(1) Fixed:      Corrected bugs cat_main_registration(2).
(2) Changed:    Adapted cat_main_registration(2) for number of template classes.
                Expect one background class if number of classes is larger than 2!
(3) Fixed:      Corrected bugs in cat_run_job and cat_main.


------------------------------------------------------------------------
r1379 | dahnke | 2018-10-22 21:05:34 +0200 (Mon, 22 Oct 2018) | 37 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_opts.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_main.m
M       cat_main_registration.m
M       cat_main_registration2.m
M       cat_run.m
M       cat_run_job.m
D       cat_run_job_APP_SPM.m
A  +    cat_run_job_APP_SPMfinal.m
A       cat_run_job_APP_SPMinit.m
D       cat_run_job_APP_final.m
M       cat_run_job_multiTPM.m
M       cat_run_newcatch.m
A       cat_spm_preproc8.m
M       cat_spm_preproc_run.m
M       cat_surf_createCS.m
M       cat_vol_headtrimming.m

(1) Fixed:      Corrected bugs in cat_vol_headtrimming GUI dependencies.
(2) Fixed:      Corrected fast surface creation face flipping in
                cat_surf_createCS.
(2) Changed:    Prepared reunion of cat_run_job and cat_run_job1070.
(3) Changed:    Extract cat_run_job_APP_SPMinit function from cat_run_job.
(4) Changed:    Renamed cat_run_job_APP_SPM to cat_run_job_APP_SPMfinal.
(5) Changed:    Updated cat_main_registration for templates with more than
                2 classes.
(6) Changed:    Added SPM accuracy variable opts.tol in cat_defaults,
                cat_run and cat_spm_preproc_run.
(7) Changed:    Updated some variables in cat_run_job_multiTPM.
(8) Fixed:      Updated cat_main_registration and cat_main to support
                templates with 3 classes.


------------------------------------------------------------------------
r1378 | gaser | 2018-10-18 16:15:29 +0200 (Thu, 18 Oct 2018) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
M       cat_run_job.m
M       cat_run_job1070.m
MM      cat_run_job_multiTPM.m

Fixed: Typos.


------------------------------------------------------------------------
r1377 | dahnke | 2018-10-18 16:04:15 +0200 (Thu, 18 Oct 2018) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_tools.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_run_job_multiTPM.m
M       cat_vol_resize.m

(1) Fixed:      Corrected bugs in cat_run_multiTPM.
                Update weighting measure.
(2) Fixed:      Corrected bugs in cat_vol_headtrimming GUI dependencies.
(3) Fixed:      Corrected problems due to wrong datatype in cat_vol_resize.
(4) Changed:    Prepared reunion of cat_run_job and cat_run_job1070.


------------------------------------------------------------------------
r1376 | gaser | 2018-10-18 15:14:22 +0200 (Thu, 18 Oct 2018) | 24 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_batch_cat.m
M       cat_conf_opts.m
M       cat_conf_tools.m
M       cat_io_senderrormail.m
M       cat_main.m
M       cat_plot_boxplot.m
M       cat_run_job.m
M       cat_stat_analyze_ROIs.m
M       check_pipeline.sh
M       check_pipeline_ROIs.m
M       html/cat.html

(1) Changed: Updated pipeline check and added TIV and global tissue values.
(2) Fixed: Corrected display of significant surface ROIs.
(3) Changed: Commented out forced transposing of data in cat_plot_boxplot
    that prevents correct display os some low-dimensional data.
(4) Fixed: Typos.
(5) Fixed: Added undefined fields spm_kamap and jacobian in cat_batch_cat.m
(6) Changed: Added pipeline check to Makefile.

------------------------------------------------------------------------
r1375 | dahnke | 2018-10-17 18:46:21 +0200 (Wed, 17 Oct 2018) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_io_volctype.m
M       cat_run_job1070.m
M       cat_run_job_multiTPM.m
M       cat_stat_check_cov2.m
M       cat_vol_headtrimming.m
M       cat_vol_sanlm.m
M       internal/cat_vol_optimizeTemplate.m

(1) Fixed:     Corrected dependency function of cat_vol_headtrimming.
(2) Changed:   Defined many images/subject data definition in cat_vol_headtrimming.
(3) Changed:   Preliminary modifications to stabilize the affine registration.
(4) Fixed:     Replaced postfix by suffix.


------------------------------------------------------------------------
r1374 | dahnke | 2018-10-16 15:46:09 +0200 (Tue, 16 Oct 2018) | 33 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_opts.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_main.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_run_job_APP_init1070.m
A       cat_run_job_multiTPM.m
M       cat_stat_histth.m
M       cat_surf_createCS.m
M       cat_vol_headtrimming.m
M       tbx_cfg_cat.m

(1)  Changed: Prepared new skull-stripping for inverse weightings
              (not use yet).
(2)  Changed: Removed gcut+ skull-stripping approach (gcutstr==2,3).
              Set gcutstr==2 by the new skull-stripping.
(3)  Changed: Set new skull-stripping as default.
(4)  Changed: Use only simplified jacobianwarped GUI entry in tbx_cfg_cat.
(5)  Fixed:   Corrected loading error of other TPMs in cat_main.
(6)  Fixed:   Corrected small bug in cat_surf_createCS (fast pipeline).
(7)  Fixed:   Corrected small bug in cat_stat_histth.
(8)  Fixed:   Corrected bug in cat_run_job_APP_ini1070.
(9)  Fixed:   Corrected problems in cat_run_job_APP_init1070.
(10) New:     Updated GUI entry in cat_conf_opts to select
              multiple TPMs in developer mode.
(11) New:     Added function cat_run_job_multiTPM to handle
              multiple TPMs in developer mode.


------------------------------------------------------------------------
r1373 | gaser | 2018-10-15 15:52:44 +0200 (Mon, 15 Oct 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_vol_headtrimming.m

Changed: Updated help text.

------------------------------------------------------------------------
r1372 | gaser | 2018-10-15 07:58:38 +0200 (Mon, 15 Oct 2018) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_tools.m
M       html/cat.html

Changed: Default interpolation for applying deformations is now trilinear to
prevent negative values due to spline interpolation for segmented images.

------------------------------------------------------------------------
r1371 | gaser | 2018-10-04 11:21:11 +0200 (Thu, 04 Oct 2018) | 67 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
MM      cat_conf_ROI.m
M       cat_conf_extopts.m
M       cat_defaults.m
MM      cat_io_findjobj.m
MM      cat_io_rmdir.m
MM      cat_main_LAS2.m
MM      cat_main_registration2.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_resamp.m
M       html/cat.html
 M      html/cat_tools_checkcov.html
 M      html/cat_tools_checkcov_exclusion.html
 M      html/icons/file_cat_log.png
 M      html/icons/file_cat_report.png
 M      html/icons/file_cat_report_surf.png
 M      html/icons/file_cat_xml.png
 M      html/icons/file_delete.png
 M      html/icons/file_delete_restore.png
 M      html/icons/file_export.png
 M      html/icons/file_new.png
 M      html/icons/file_open.png
 M      html/icons/file_pdf.png
 M      html/icons/file_print.png
 M      html/icons/file_save.png
 M      html/icons/file_search.png
 M      html/icons/file_spm_view.png
 M      html/icons/file_surf.png
 M      html/icons/file_surfc.png
 M      html/icons/redo.png
 M      html/icons/refresh.png
 M      html/icons/settings.png
 M      html/icons/status_failed.png
 M      html/icons/status_forbiden.png
 M      html/icons/status_help.png
 M      html/icons/status_help2.png
 M      html/icons/status_info.png
 M      html/icons/status_passed.png
 M      html/icons/status_warning_hard.png
 M      html/icons/status_warning_soft.png
 M      html/icons/tool_data_cursor.png
 M      html/icons/tool_fit.png
 M      html/icons/tool_hand.png
 M      html/icons/tool_zoom_in.png
 M      html/icons/tool_zoom_out.png
 M      html/icons/trash_auto.png
 M      html/icons/trash_col_add.png
 M      html/icons/trash_col_rm.png
 M      html/icons/trash_row_add.png
 M      html/icons/trash_row_rm.png
 M      html/icons/trash_tip_add.png
 M      html/icons/trash_tip_rm.png
 M      html/icons/undo.png
 M      html/images/cat_stat_checkcov_00_overview.png
 M      html/images/cat_stat_checkcov_01_batch.png
 M      html/images/cat_stat_checkcov_02_command.png
 M      html/images/cat_stat_checkcov_03_checkcov.png
 M      html/images/cat_stat_checkcov_04_boxplot01_MNC.png
 M      html/images/cat_stat_checkcov_04_boxplot02_IQR.png
 M      html/images/cat_stat_checkcov_05_check_01_original.png
 M      html/images/cat_stat_checkcov_07_exclusion.png

(1) Changed: Added Holm-Bonferroni correction again to ROI analysis.
(2) Changed: Corrected typos.

------------------------------------------------------------------------
r1370 | dahnke | 2018-10-04 10:38:09 +0200 (Thu, 04 Oct 2018) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_io_colormaps.m
M       cat_main.m
M       cat_stat_check_cov2.m
M       cat_vol_sanlm.m
M       tbx_cfg_cat.m

(1) Fixed:  Corrected bug in cat_stat_check_cov2.
(2) Fixed:  Corrected bugs in cat_vol_sanlm.
(3) Fixed:  Corrected problems of new skull-stripping in cat_main.
(4) New:    Added color overlay for label map in cat_stat_check_cov2.


------------------------------------------------------------------------
r1369 | dahnke | 2018-10-01 13:53:15 +0200 (Mon, 01 Oct 2018) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main.m

(1) New:  Added new skull-stripping method APRG (adaptive probability
          region-growing) that refines the probability maps of the SPM
          approach by region-growing techniques of the gcut approach
          with a final surface-based optimization strategy.




------------------------------------------------------------------------
r1368 | dahnke | 2018-09-28 12:04:52 +0200 (Fri, 28 Sep 2018) | 31 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_main.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_stat_check_cov2.m
M       cat_stat_histth.m
M       cat_vol_headtrimming.m
M       html/style.css
M       kmeans3D.m
M       tbx_cfg_cat.m

(1) Fixed:      Corrected new problem in cat_stat_histth with
                strong outliers.
(2) Changed:    Added warning if no skull-stripping is used
                (gcutstr=-1) but skull was detected.
(3) Fixed:      Corrected bugs in kamap pipeline in cat_main.
(4) Fixed:      Corrected boundary bugs in style.css that makes
                HTML page to wide and active the horizontal scroll
                bar. The major white 10px boundary depends on the
                SPM Graphics figure properties.
(5) Changed:    Activate native label output in cat_defaults.
(6) Changed:    Simplified output fiels in segment GUI.
(7) Changed:    Modified head trimming GUI.




------------------------------------------------------------------------
r1367 | dahnke | 2018-09-26 12:44:47 +0200 (Wed, 26 Sep 2018) | 44 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_main.m
A       cat_main_registration2.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_stat_check_cov.m
M       cat_stat_check_cov2.m
M       cat_stat_histth.m
M       cat_vol_sanlm.m
A       html/cat_tools_checkcov_exclusion.html
A       html/images/cat_stat_checkcov_00_overview.png
A       html/images/cat_stat_checkcov_01_batch.png
A       html/images/cat_stat_checkcov_02_command.png
A       html/images/cat_stat_checkcov_03_checkcov.png
A       html/images/cat_stat_checkcov_04_boxplot01_MNC.png
A       html/images/cat_stat_checkcov_04_boxplot02_IQR.png
A       html/images/cat_stat_checkcov_05_check_01_original.png
A       html/images/cat_stat_checkcov_07_exclusion.png

(1) Changed:    Further development of cat_stat_check_cov that is
                (only) available via batch tools. Corrected many
                bugs and added many functions, especially the data
                exclusion window and the data moving function.
                Created a first version of the HTML help page.
(2) Changed:    Added new_version of cat_main_registration that
                include further settings to handle brains with
                very large ventricles (still in development).
                Moreover, spline interpolation rather linear
                interpolation is used. Not finish!
(3) Fixed:      Corrected small bug in k-means AMAP pipeline.
(4) Fixed:      Corrected problem in cat_vol_sanlm filter with
                adding noise to zero (skull-stripped) background.
(5) Fixed:      Corrected problem in cat_stat_histth with strong
                outliers.
(6) New:        Added no skull-stripping option for gcutstr that
                overwrite the automatic skull-stripping detection
                in cat_run_job(1070).


------------------------------------------------------------------------
r1366 | dahnke | 2018-09-21 12:23:17 +0200 (Fri, 21 Sep 2018) | 77 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
A       cat_io_findjobj.m
A       cat_io_rmdir.m
M       cat_main.m
A       cat_main_LAS2.m
M       cat_plot_boxplot.m
M       cat_run.m
M       cat_stat_check_SPM.m
A       html/cat_tools_checkcov.html
A       html/icons
A       html/icons/file_cat_log.png
A       html/icons/file_cat_report.png
A       html/icons/file_cat_report_surf.png
A       html/icons/file_cat_xml.png
A       html/icons/file_delete.png
A       html/icons/file_delete_restore.png
A       html/icons/file_export.png
A       html/icons/file_new.png
A       html/icons/file_open.png
A       html/icons/file_pdf.png
A       html/icons/file_print.png
A       html/icons/file_save.png
A       html/icons/file_search.png
A       html/icons/file_spm_view.png
A       html/icons/file_surf.png
A       html/icons/file_surfc.png
A       html/icons/redo.png
A       html/icons/refresh.png
A       html/icons/settings.png
A       html/icons/status_failed.png
A       html/icons/status_forbiden.png
A       html/icons/status_help.png
A       html/icons/status_help2.png
A       html/icons/status_info.png
A       html/icons/status_passed.png
A       html/icons/status_warning_hard.png
A       html/icons/status_warning_soft.png
A       html/icons/tool_data_cursor.png
A       html/icons/tool_fit.png
A       html/icons/tool_hand.png
A       html/icons/tool_zoom_in.png
A       html/icons/tool_zoom_out.png
A       html/icons/trash_auto.png
A       html/icons/trash_col_add.png
A       html/icons/trash_col_rm.png
A       html/icons/trash_row_add.png
A       html/icons/trash_row_rm.png
A       html/icons/trash_tip_add.png
A       html/icons/trash_tip_rm.png
A       html/icons/undo.png
M       html/style.css
M       kmeans3D.m

(1) Fixed:      Corrected background segmentation bug in cat_main!
(2) New:        Added new_release option in developer GUI that is
                not available in the cat_defaults and therefore
                defined in the cat_run.
(3) New:        Added new segmentation approach that replaces the
                brain tissue segmentation of SPM by the k-means
                AMAP (developer, new_release). Added variable
                cat.extops.spm_kamap in cat_defaults.
(4) Changed:    Restructured cat_main_LAS and added documentation
                (new_release). Corrected bug in background/CSF
                handling.
(5) Fixed:      Corrected bug in case of no selected files in
                cat_stat_check_SPM.
(6) Changed:    Corrected small bugs and added help in kmeans3D.
(7) Changed:    Added CSS style for centered HTML help figures.
(8) Changed:    Small changes in cat_plot_boxplot to improve
                output of label values.
(9) Changed:    JPG export of the CAT report in cat_main for
                cat_stat_check_cov2.


------------------------------------------------------------------------
r1365 | gaser | 2018-09-12 14:08:04 +0200 (Wed, 12 Sep 2018) | 11 lines

Changed paths:
M       CHANGES.txt
A       cat_conf_ROI.m
M       cat_conf_long.m
M       cat_long_main.m
M       cat_long_multi_run.m
M       tbx_cfg_cat.m

(1) Changed: Added ROI options to longitudinal pipeline.
(2) Changed: Moved ROI config options to a seperate file cat_conf_ROI.m

------------------------------------------------------------------------
r1364 | gaser | 2018-09-11 10:23:03 +0200 (Tue, 11 Sep 2018) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_long.m
M       html/cat.html

Changed: Removed wrong print flag in cat_batch_long.m

------------------------------------------------------------------------
r1363 | gaser | 2018-09-02 16:40:07 +0200 (Sun, 02 Sep 2018) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_createCS.m
M       html/cat.html

Fixed: Removed debugging code in cat_surf_createCS.m that caused crash
(thanks to Larry Lai for pointing to that issue).

------------------------------------------------------------------------
r1362 | gaser | 2018-08-31 10:47:29 +0200 (Fri, 31 Aug 2018) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       html/cat.html
M       spm_cat12.m

Changed: Updated version information to CAT12.5.

------------------------------------------------------------------------
r1361 | gaser | 2018-08-31 10:44:57 +0200 (Fri, 31 Aug 2018) | 18 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_batch_cat.sh
M       cat_batch_long.sh
M       cat_batch_spm.sh
M       cat_main.m
M       cat_surf_createCS.m
M       check_pipeline.sh
M       distribute_to_server.sh

(1) Fixed: Changed shell command scripts to "bash" because "sh" sometimes
    caused problems (thanks to Vincent Koppelmann for pointing to that
    issue).
(2) Changed: Added Yp0 as input for cat_surf_createCS which is used to
    optionally refine pial and white matter surface.

------------------------------------------------------------------------
r1360 | gaser | 2018-08-29 15:49:24 +0200 (Wed, 29 Aug 2018) | 19 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_main.m
M       cat_surf_createCS.m
M       cat_surf_results.m
M       html/cat.html

(1) Changed: Unused menus and options in cat_surf_results.m are now disabled
    instead of not visible.
(2) Changed: Lights for rendering are changed in cat_surf_results.m
(3) Fixed: optional use of kmeans was not working in cat_main.m.
(4) Changed: Added some new options to extract pial and white matter surface
    which is still very slow, but might be helpful for mapping ultra-high
    resolution data (still experimental).
(5) Changed: Use inverse deformation to map fsavg mask to native surface data
    to prevent unreliable values in subcortical areas.

------------------------------------------------------------------------
r1359 | gaser | 2018-08-17 14:09:22 +0200 (Fri, 17 Aug 2018) | 6 lines

Changed paths:
M       CHANGES.txt

(1) Changed: Added new flag to CAT_DeformSurf command in cat_surf_createCS.m
(2) Changed: Updated new binaries because of new flag for CAT_DeformSurf.

------------------------------------------------------------------------
r1358 | gaser | 2018-08-17 14:06:57 +0200 (Fri, 17 Aug 2018) | 1 line


------------------------------------------------------------------------
r1357 | gaser | 2018-08-17 14:03:21 +0200 (Fri, 17 Aug 2018) | 6 lines

Changed paths:
M       CHANGES.txt

(1) Changed: Added new flag to CAT_DeformSurf command in cat_surf_createCS.m
(2) Changed: Updated new binaries because of new flag for CAT_DeformSurf.

------------------------------------------------------------------------
r1356 | gaser | 2018-08-17 14:02:44 +0200 (Fri, 17 Aug 2018) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_createCS.m
MM      check_pipeline_ROIs.m
M       html/cat.html

(1) Changed: Added new flag to CAT_DeformSurf command in cat_surf_createCS.m
(2) Changed: Updated new binaries because of new flag for CAT_DeformSurf.

------------------------------------------------------------------------
r1355 | gaser | 2018-08-13 15:53:48 +0200 (Mon, 13 Aug 2018) | 12 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat12.m
M       cat_update.m
MM      check_pipeline.sh
M       html/cat_versions.html

(1) Changed: Added some handling for deployed (compliled) CAt12 version.
(2) Changed: Updated CAT12 manual and online help.

------------------------------------------------------------------------
r1354 | gaser | 2018-08-13 12:21:10 +0200 (Mon, 13 Aug 2018) | 23 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_surf_results.m
M       check_pipeline.sh
A       check_pipeline_ROIs.m
M       html/cat.html
M       html/cat_methods_SBM.html
M       html/cat_tools_VBM.html
M       html/cat_versions.html
M       spm_cat12.m
M       tbx_cfg_cat.m

(1) Fixed: Crahs in cat_surf_results due to typo.
(2) Changed: Updated version information to CAT12.5-rc1.
(3) Changed: Updated online help text and CAT12 manual.
(4) Changed: Default interpolation is now "Fixed 1 mm" in cat_defaults.

------------------------------------------------------------------------
r1353 | dahnke | 2018-08-13 10:19:19 +0200 (Mon, 13 Aug 2018) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       html/cat_methods_SBM.html
M       html/cat_methods_VBM.html
M       html/cat_tools_VBM.html

(1) Fixed:  Removed bug in cat_conf_extopts.
(2) Fixed:  Corrected and updated help HTML texts.
            Combined Skull-Stripping and Cleanup in cat_methods_vbm
            and removed references to variables that were not used
            anymore. Updated surface measures text in cat_methods_SBM.
            Added help text for head trimming tool and data type
            converter in cat_tools_VBM.

------------------------------------------------------------------------
r1352 | dahnke | 2018-08-10 18:11:27 +0200 (Fri, 10 Aug 2018) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_stat_check_cov2.m
M       kmeans3D.m

(1) Fixed:      Corrected behavior in case of NaNs in kmeans3d.
(2) Changed:    Modified default-user resolution GUI.
(3) Changed:    Added jpg-report output in cat_main for later
                use in cat_stat_check_cov2.
(4) Changed:    Further development of cat_stat_check_cov2.


------------------------------------------------------------------------
r1351 | gaser | 2018-08-09 14:09:01 +0200 (Thu, 09 Aug 2018) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_cat.m
M       cat_main.m
M       cat_surf_results.m
A       check_pipeline.sh
M       distribute_to_server.sh
M       html/cat.html

(1) Changed: Disable some data cursor functions in cat_surf_results.m if no
    SPM.mat file was found.
(2) Fixed: Some graphical output in cat_main.m was not possible for running
    cat from the shell command line with cat_batch_cat.sh.
(3) Fixed: The flag redspmres was not yet considered in cat_batch_cat.m.

------------------------------------------------------------------------
r1350 | gaser | 2018-08-07 11:56:11 +0200 (Tue, 07 Aug 2018) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_cat.m
M       cat_conf_tools.m
M       cat_roi_fun.m
M       html/cat.html

(1) Fixed: In cat_roi_fun.m current directory is used if output directory
    field is empty.
(2) Fixed: New fields added that have to be considered in cat_batch_cat.m.

------------------------------------------------------------------------
r1349 | dahnke | 2018-08-06 18:59:14 +0200 (Mon, 06 Aug 2018) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_registration.m
M       cat_stat_check_cov.m
M       cat_stat_check_cov2.m

(1) Fixed:   Corrected errors in spatial registration in cat_main and
             cat_main_registration.
(2) Changed: Further development of cat_stat_check_cov2.


------------------------------------------------------------------------
r1348 | gaser | 2018-08-02 15:01:57 +0200 (Thu, 02 Aug 2018) | 10 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_run_job1070.m
M       html/cat_versions.html

(1) Changed: Updated CAT12 manual and online help.
(2) Fixed: Typos

------------------------------------------------------------------------
r1347 | dahnke | 2018-08-02 12:59:46 +0200 (Thu, 02 Aug 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_run_job1070.m
M       cat_stat_check_cov2.m

(1) Fixed:  Problematic skull-stripping part 2.

------------------------------------------------------------------------
r1346 | dahnke | 2018-08-02 11:42:11 +0200 (Thu, 02 Aug 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_main.m

(1) Fixed:  Corrected colorbar in other figure printing bug in cat_main.

------------------------------------------------------------------------
r1345 | gaser | 2018-08-02 11:37:11 +0200 (Thu, 02 Aug 2018) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_tools.m
M       cat_defaults.m
MM      cat_stat_check_cov2.m
M       html/cat.html

(1) Changed: Added Eulcer number and size of topology defects to
    cat_stat_check_cov2.m
(2) Fixed: Typos

------------------------------------------------------------------------
r1344 | dahnke | 2018-08-02 11:13:13 +0200 (Thu, 02 Aug 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m

(1) Fixed:  Small changes to correct and optimize other calls of clean_gwc.

------------------------------------------------------------------------
r1343 | dahnke | 2018-08-02 10:41:03 +0200 (Thu, 02 Aug 2018) | 26 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_stat_check_cov.m
A       cat_stat_check_cov2.m
M       cat_vol_sanlm.m

(1) Fixed:  Corrected the optimized call of cleanup in SPM Preprocessing 2
            that strongly influence the skull-stripping of CAT.
            Thanks to Ying-Liang Lai for pointing out that issue.
(2) Fixed:  Corrected bug in runtime estimation that avoid counting of
            early processing steps in cat_run_job(1070).
(3) New:    Added alpha version of cat_stat_check_cov2 that is called from
            cat_stat_check_cov in the development user mode. Although it
            based on the previous version it include large changes:
             - automatic detection of XML and other report files
             - group-specific symbols and legend in Mahalanobis plot
             - new GUI elements for navigation, data checking and
               removal of outliers
             - percentage scaling rather than school marks
             - good values always on the top of the boxplot
             - many further layout changes


------------------------------------------------------------------------
r1342 | gaser | 2018-07-30 10:09:14 +0200 (Mon, 30 Jul 2018) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       cat_main_gintnorm.m
M       cat_stat_check_cov.m
M       cat_vol_partvol.m
M       html/cat.html

(1) Fixed: Division by zero issues in cat_vol_partvol.m
(2) Fixed: check for additional quality measures crashed for volumes in
    cat_stat_check_cov.m
(3) Fixed: Out of range issue in cat_main_gintnorm.m and cat_main.m.

------------------------------------------------------------------------
r1341 | dahnke | 2018-07-27 15:14:51 +0200 (Fri, 27 Jul 2018) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_opts.m
M       cat_defaults.m
M       cat_main.m
M       cat_plot_boxplot.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_vol_qa.m

1) Fixed:   Corrected mark2rps function to consider NaNs.
2) Fixed:   Corrected extopts.redspmres to opts.redspmres.



------------------------------------------------------------------------
r1340 | gaser | 2018-07-25 15:43:27 +0200 (Wed, 25 Jul 2018) | 6 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt

Changed: Updated CAT12 manual.

------------------------------------------------------------------------
r1339 | gaser | 2018-07-25 15:35:02 +0200 (Wed, 25 Jul 2018) | 20 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_long.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_long_main.m
M       cat_long_multi_run.m
M       cat_stat_check_cov.m
M       cat_surf_createCS.m
MM      cat_vol_headtrimming.m
M       html/cat_versions.html

(1) Changed: Added expert field for longitudinal pipeline to keep temporary
    files that are usually removed after processing.
(2) Fixed: Expert options are now also used in longitudinal pipeline.
(3) Fixed: Corrected typos.

------------------------------------------------------------------------
r1338 | dahnke | 2018-07-23 14:51:04 +0200 (Mon, 23 Jul 2018) | 24 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_opts.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_tst_qa_cleaner.m
M       cat_vol_headtrimming.m
M       cat_vol_partvol.m
M       cat_vol_resize.m

1) Fixed:   Corrected bugs in cat_vol_trimmer.
2) Update:  Added resolution limitation for SPM preprocessing
            for more stable and faster processing that is
            controlled by the extopts.redspmres parameter.
            This further include small changes in cat_main,
            cat_run_job(1070) and cat_vol_resize.
3) Fixed:   Corrected bugs in cat_vol_LAS.



------------------------------------------------------------------------
r1337 | dahnke | 2018-07-19 19:34:21 +0200 (Thu, 19 Jul 2018) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_io_volctype.m
A       cat_vol_headtrimming.m
M       cat_vol_sanlm.m

1) New:     Added batch to optimize images by removing surrounding
            empty voxels with air.

------------------------------------------------------------------------
r1336 | gaser | 2018-07-19 16:29:40 +0200 (Thu, 19 Jul 2018) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_main.m
M       cat_surf_createCS.m

(1) Changed: Added size of topology defects to "Image and Processing Quality"
    output in pdf-report and xml-file.
(2) Changed: Removed unncessary code for reduceCS in cat_surf_createCS.m

------------------------------------------------------------------------
r1335 | dahnke | 2018-07-18 19:11:28 +0200 (Wed, 18 Jul 2018) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_main.m
M       cat_run_job.m
M       cat_run_job1070.m

1) Fixed:    Corrected error if no registration was required.
2) Fixed:    Corrected error in SLC in case of internal interpolation.
3) Fixed:    Corrected errors in CAT12 SPM Segmentation pipeline.


------------------------------------------------------------------------
r1334 | gaser | 2018-07-18 16:26:02 +0200 (Wed, 18 Jul 2018) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_surf_createCS.m
M       cat_vol_qa.m
 M      templates_1.50mm/cat_strokelesions_ATLAS303.nii

Changed: Added Euler number to "Image and Processing Quality" output in
pdf-report.

------------------------------------------------------------------------
r1333 | gaser | 2018-07-18 11:13:15 +0200 (Wed, 18 Jul 2018) | 17 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_conf_extopts.m
M       cat_main.m
M       cat_surf_createCS.m
 M      cat_vol_maskimage.m
M       cat_vol_partvol.m
M       html/cat.html
M       html/cat_methods_VBM_APP.html
M       spm_cat12.m

(1) Changed: Set version numbering to CAT 12.4.
(2) Changed: Corrected typos.
(3) Changed: Added absolute Euler number for quality assurance.

------------------------------------------------------------------------
r1332 | dahnke | 2018-07-17 16:44:14 +0200 (Tue, 17 Jul 2018) | 27 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_run.m
M       cat_run_job1070.m
M       cat_vol_partvol.m
M       html/cat_methods_VBM.html
M       html/cat_methods_VBM_APP.html
M       tbx_cfg_cat.m
A       templates_1.50mm/cat_strokelesions_ATLAS303.nii

1) Changed:   Created a separate field to handle stroke lesion
              correction (SLC) and writing of stroke lesion maps
              in the expert GUI and the defaults-file with:
                  0 - no
                  1 - manual
2) New:       Added error message in cat_run if output of stroke
              lesion or WMH maps is active but WMHC or SLC is
              turned off. Added warning in case of manual SLC
              but not manual defined areas were found in the
              input image.
3) Changed:   Updated APP and skull-stripping GUI and HTML help.


------------------------------------------------------------------------
r1331 | gaser | 2018-07-17 10:16:48 +0200 (Tue, 17 Jul 2018) | 11 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_defaults.m
M       cat_main.m

(1) Changed: WMH handling is now again set to correction for Dartel/Shooting
    registration.
(2) Changed: Corrected typos.

------------------------------------------------------------------------
r1330 | dahnke | 2018-07-13 09:38:04 +0200 (Fri, 13 Jul 2018) | 29 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_main.m
M       cat_main_registration.m
M       cat_run_job.m
M       cat_run_job1070.m
A       cat_vol_maskimage.m
M       cat_vol_partvol.m
M       tbx_cfg_cat.m

1) Fixed:       Corrected small bugs in tbx_cfg_cat and cat_conf_tools.
2) New:         Added function cat_vol_maskimage for lesion masking to
                avoid deformation in these areas.
3) New:         Added detection of manual defined lesions (zero values)
                in cat_run_job(1070) in case of active lesion handling.
                Removed similar steps in cat_main and differentiate
                between registration with(out) manual lesion data.
                Added handling for output of lesion maps.
4) Fixed:       Deactivated additional calls of spm_preproc8 with masked
                regions that sometimes strongly increased processing time
                (thanks to Gabriel Ziegler for pointing out that issue).
5) Changed:     Updated automatic stroke lesion detection in
                cat_vol_partvol by detecting large untypical CSF areas
                (and strongly (asymmetric) deformed regions), followed by
                a region-growing. The detection of asymmetric regions is
                defined in cat_main but is inactive because it works only
                in single cases yet.

------------------------------------------------------------------------
r1329 | gaser | 2018-07-05 21:11:46 +0200 (Thu, 05 Jul 2018) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m

Changed: Dartel or Shooting registration is currently always necessary because
of new developmental code in cat_main_registration. This will be solved in
newer releases.

------------------------------------------------------------------------
r1328 | gaser | 2018-07-05 20:15:55 +0200 (Thu, 05 Jul 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m

Fixed: Disabled manual lesion masking because of missing cat_vol_maskimage.m

------------------------------------------------------------------------
r1327 | gaser | 2018-07-05 00:14:33 +0200 (Thu, 05 Jul 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_long_APP.m

Fixed: APP selection was not considered in longitudinal pipeline.

------------------------------------------------------------------------
r1326 | gaser | 2018-06-25 17:04:24 +0200 (Mon, 25 Jun 2018) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_install_atlases.m
M       cat_main.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_vol_slice_overlay.m
M       html/cat.html

(1) Fixed: Atlas installation was incorrect (Thanks to Ramesh Babu for
    pointing to that bug).
(2) Changed: Corrected typos.

------------------------------------------------------------------------
r1325 | dahnke | 2018-06-20 19:57:53 +0200 (Wed, 20 Jun 2018) | 48 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_io_colormaps.m
M       cat_main.m
M       cat_main_registration.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_surf_render2.m
M       cat_vol_partvol.m
M       ds.m
M       tbx_cfg_cat.m

PART A - WMHs:
1) Changed:     Removed WMHCstr parameter from expert GUI to focus on the
                standard case (changed to 0.5 in cat_defaults).
2) Changed:     Moved WMHC correction after AMAP processing (cat_main).
                WMH regions were now handled as GM in the initial AMAP
                segmentation. After AMAP all GM voxels in WMH regions were
                set as GM (WMHC<2), WM (WMHC=2) or as extra class (WMHC=3).
                Added warnings in case of bad combinations of WMHC and
                WMHCstr that use no correction but output images.
3) Changed:     The WMHs required an updated of the internal scaling of
                Yp0b in cat_main from 3 to 5 classes to have round uint8
                values of a tissue class, ie. with a WM value of 255/5*3.

PART B - Lesion handling controlled by WMHC:
1) New:         Added further cases to the WMHC parameter to handle the
                lesion processing (WMHC=4). Added a simple detection of
                very large lesion in cat_vol_partvol (WMHC=5).
2) New:         Added lesion handling by zero values in the original
                dataset that were now ignored in the Dartel/Shooting
                deformation process (cat_main_registration).
3) New:         Because of the internal interpolation the detection of
                manual lesions (zero values in the brain) is located in
                the cat_run_job(1070).
4) New:         Added batch for lesion and brain masking (cat_conf_tools).

PART C - Other changes:
1) Changed:     Removed some gcutstr expert options because of to many
                options and to unspecific/small/useless changes.
2) Changed:     Small cleanup and modifications in cat_io_colormaps.
3) Fixed:       Corrected small bug in cat_surf_render2.



------------------------------------------------------------------------
r1324 | gaser | 2018-06-14 17:07:25 +0200 (Thu, 14 Jun 2018) | 8 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       html/cat_methods_FN.html

Changed: Updated CAT12 manual and online help.

------------------------------------------------------------------------
r1323 | gaser | 2018-06-11 15:11:34 +0200 (Mon, 11 Jun 2018) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_long.m
M       cat_main_LAS.m
M       cat_surf_createCS.m
M       cat_vol_sanlm.m
M       html/cat.html

(1) Changed: Optimized memory management in cat_main_LAS.
(2) Changed: Removed option for thickness estimation (for ROI analysis only)
    from longitudinal pipeline.

------------------------------------------------------------------------
r1322 | dahnke | 2018-05-26 18:39:41 +0200 (Sat, 26 May 2018) | 25 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Contents_info.txt
M       cat_conf_extopts.m
M       cat_conf_tools.m
M       cat_main.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_surf_createCS.m
D       cat_vol_isarnlm.m
M       cat_vol_partvol.m
M       cat_vol_sanlm.m
M       development/cat_surf_createCS.m
M       html/cat_tools_VBM.html
M       internal/cat_tst_prepareManualSegmentation.m
M       internal/cat_vol_nlmus.m

Changed:    Added resolution reduced filtering to SANLM filter.
Changed:    Removed ISARNLM filter and replaced previous calls
            by the new SANLM filter.
Changed:    Updated SANLM calls in cat_run_job* and cat_main.
Changed:    Updated NLM GUI and documentation.


------------------------------------------------------------------------
r1321 | gaser | 2018-05-24 23:28:30 +0200 (Thu, 24 May 2018) | 8 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt

Fixed: Some of the shown design matrices in the CAT12 manual were not correct.


------------------------------------------------------------------------
r1320 | gaser | 2018-05-24 12:08:34 +0200 (Thu, 24 May 2018) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_long_main.m
M       cat_vol_groupwise_ls.m
M       cat_vol_series_align.m
M       html/cat.html

Changed: Added option to use final brainmask in longitudinal rigid registration.


------------------------------------------------------------------------
r1319 | dahnke | 2018-05-23 14:11:55 +0200 (Wed, 23 May 2018) | 29 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_registration.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_tst_calc_kappa.m
M       cat_vol_grad.m
M       cat_vol_morph.m
M       cat_vol_partvol.m

Fixed:      Corrected small bug in cat_run_registration.
Fixed:      Added missed variable in cat_run_job and cat_run_job1070.
Fixed:      Corrected bug in fast Shooting registration (cat_main:678).
Changed:    Further option in cat_vol_grad.
Changed:    Small modifications in cat_tst_calc_kappa.
Changed:    Small modifications in cat_vol_morph.
Changed*:   Large modifications of the WMH detection in cat_part_vol.
            Tested for MICCAI2017 WMH data with/without FLAIR input:
                CAT     (T1)     DSC 0.5824�0.1705  gtt1
                CAT     (T1+FL)  DSC 0.5235�0.2013  gtt1
                LST-LGA (T1+FL)  DSC 0.6186�0.1539  gtt1
                LST-LPA (FL)     DSC 0.6172�0.2003  gto
            with gtt1 as T1-optimized ground truth with intensity limit
            and gto as original FLAIR-based ground truth.




------------------------------------------------------------------------
r1318 | gaser | 2018-05-14 12:39:58 +0200 (Mon, 14 May 2018) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_run_job.m
M       html/cat.html
 M      templates_1.50mm/cat_wmh_miccai2017.nii

Fixed: Removed error in cat_run_job caused by undefined variable (thanks to
Larry Lai for pointing to this error).

------------------------------------------------------------------------
r1317 | gaser | 2018-05-09 12:32:45 +0200 (Wed, 09 May 2018) | 22 lines

Changed paths:
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_install_atlases.m
M       cat_main.m
M       cat_roi_fun.m
M       cat_stat_analyze_ROIs.m
M       cat_vol_atlas.m
M       html/cat.html
D       templates_1.50mm/labels_dartel_aal.xml
D       templates_1.50mm/labels_dartel_cobra.xml
D       templates_1.50mm/labels_dartel_hammers.xml
D       templates_1.50mm/labels_dartel_ibsr.xml
D       templates_1.50mm/labels_dartel_lpba40.xml
D       templates_1.50mm/labels_dartel_mori.xml
D       templates_1.50mm/labels_dartel_neuromorphometrics.xml

(1) Removed: Removed old ROI-xml files that are now converted from csv
    using cat_install_atlases.m
(2) Changed: Implemented conversion from CSV to xml in cat_install_atlases.m

------------------------------------------------------------------------
r1316 | dahnke | 2018-05-03 18:32:07 +0200 (Thu, 03 May 2018) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_vol_approx.m
M       cat_vol_morph.m
M       cat_vol_partvol.m
M       tbx_cfg_cat.m
 M      templates_1.50mm/cat_wmh.nii
A       templates_1.50mm/cat_wmh_miccai2017.nii

New:        Added additional developer-GUI entry for FLAIR input
            images for WMH segmentation.


------------------------------------------------------------------------
r1315 | dahnke | 2018-05-03 11:34:57 +0200 (Thu, 03 May 2018) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_gcut.m
M       cat_vol_morph.m
M       cat_vol_partvol.m
M       templates_1.50mm/cat_wmh.nii

Changed:        Updated WMH segmentation for new atlas maps.
Changed:        Updated cat_wmh atlas.
New:            Added MICCAI2017 WMH atlas.
Fixed:          Corrected bug in cat_main_gcut.



------------------------------------------------------------------------
r1314 | gaser | 2018-05-03 09:07:58 +0200 (Thu, 03 May 2018) | 22 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
M       cat_plot_boxplot.m
M       html/cat.html
M       html/cat_methods_VBM.html
M       html/cat_versions.html
M       tbx_cfg_cat.m
M       templates_1.50mm/cobra.csv
M       templates_1.50mm/cobra.nii
M       templates_1.50mm/cobra.txt

(1) Changed: Updaed and extended Cobra atlas. See
    cat12/templates_1.50mm/cobra.txt for more information.
(2) Changed: Updated online help and CAT12 manual.
(3) Changed: Added option for internal interpolation to default GUI.

------------------------------------------------------------------------
r1313 | dahnke | 2018-04-30 18:44:18 +0200 (Mon, 30 Apr 2018) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_partvol.m
A       templates_1.50mm/cat_wmh.nii
 M      templates_animals/chimpanzee_atlas_davi.nii
 M      templates_animals/chimpanzee_cat.nii
 M      templates_animals_surfaces/lc.central.Template_chimpanzee_T1_GS.gii
 M      templates_animals_surfaces/lc.thickness.Template_chimpanzee_T1_GS
 M      templates_animals_surfaces/lh.central.Template_chimpanzee_T1_GS.gii
 M      templates_animals_surfaces/lh.thickness.Template_chimpanzee_T1_GS
 M      templates_animals_surfaces/mesh.central.Template_chimpanzee_T1_GS.gii
 M      templates_animals_surfaces/rc.central.Template_chimpanzee_T1_GS.gii
 M      templates_animals_surfaces/rc.thickness.Template_chimpanzee_T1_GS
 M      templates_animals_surfaces/rh.central.Template_chimpanzee_T1_GS.gii
 M      templates_animals_surfaces/rh.thickness.Template_chimpanzee_T1_GS




------------------------------------------------------------------------
r1312 | dahnke | 2018-04-30 14:34:52 +0200 (Mon, 30 Apr 2018) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_main.m
M       cat_vol_morph.m
M       cat_vol_partvol.m
M       ds.m

(1) Fixed:      Corrected small bug in cat_vol_morph.
(2) Changed:    Set Shooting-based skull-stripping as default (gcut==2).
(3) Changed:    Modified WMH correction in cat_vol_part and cleaned code.


------------------------------------------------------------------------
r1311 | dahnke | 2018-04-26 10:16:03 +0200 (Thu, 26 Apr 2018) | 32 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_surf_info.m
M       cat_surf_render2.m
M       cat_surf_vol2surf.m
M       cat_vol_pbt.m
MM      cat_vol_pbt3.m
M       spm_cat12.m
M       templates_animals/chimpanzee_TPM.nii
A       templates_animals/chimpanzee_atlas_davi.nii
A       templates_animals/chimpanzee_cat.nii
A       templates_animals_surfaces
A       templates_animals_surfaces/lc.central.Template_chimpanzee_T1_GS.gii
A       templates_animals_surfaces/lc.thickness.Template_chimpanzee_T1_GS
A       templates_animals_surfaces/lh.central.Template_chimpanzee_T1_GS.gii
A       templates_animals_surfaces/lh.thickness.Template_chimpanzee_T1_GS
A       templates_animals_surfaces/mesh.central.Template_chimpanzee_T1_GS.gii
A       templates_animals_surfaces/rc.central.Template_chimpanzee_T1_GS.gii
A       templates_animals_surfaces/rc.thickness.Template_chimpanzee_T1_GS
A       templates_animals_surfaces/rh.central.Template_chimpanzee_T1_GS.gii
A       templates_animals_surfaces/rh.thickness.Template_chimpanzee_T1_GS

(1) Fixed:      Corrected bugs in cat_surf_render2 & cat_surf_info.
(2) New:        Added chimpanzee surface Shooting templates.
(3) Changed:    Updated help of cat_surf_vol2surf and added
                cerebellum mapping (default=0).
(4) Fixed:      Prevent output of gyrus-/sulcus-width in the
                cat_report if they  were not processed (NaN).
(5) Fixed:      Temporary replaced chimpanzee TPM with greater apes
                TPM due to an data type error of the chimpanzee TPM.

------------------------------------------------------------------------
r1310 | dahnke | 2018-04-25 15:55:32 +0200 (Wed, 25 Apr 2018) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat_io_volctype.m
M       cat_main.m
M       cat_run_job1070.m
M       cat_surf_vol2surf.m
M       cat_vol_div.m
M       cat_vol_grad.m
M       cat_vol_pbt3.m
M       templates_animals/chimpanzee_TPM.nii

(1) Changed:      Set harder brain mask for surface reconstruction
                  in cat_main!
(2) Changed:      Updated help and default settings in cat_surf_vol2surf.
(3) Changed:      Updated help and add further parameter in cat_vol_div.
(4) Fixed:        Corrected bugs in cat_io_volctype (4D data).
(5) Fixed:        Corrected bugs in cat_run_job1070 (primate processing).


------------------------------------------------------------------------
r1309 | dahnke | 2018-04-23 16:19:28 +0200 (Mon, 23 Apr 2018) | 31 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_defaults.m
M       cat_get_defaults.m
M       cat_main.m
M       cat_stat_histth.m
M       cat_surf_createCS.m
M       cat_surf_info.m
M       cat_surf_render2.m
M       cat_vol_morph.m
A       cat_vol_pbt3.m
M       cat_vol_pbtv.cpp
M       cat_vol_pbtv.mexmaci64
M       ds.m
M       spm_cat12.m
M       tbx_cfg_cat.m

(1) Fixed:      Corrected small bugs in cat_surf_info, cat_stat_histth and
                cat_vol_morph.
(2) Changed:    Updated output of Matlab surfaces in cat_surf_render2.
(3) Changed:    Set Neuromorphometrics as only active atlas by default.
(4) Fixed:      Corrected bug with atlas GUI in spm_cat12/cat12 and updated
                help creation in tbx_cfg_cat to include only atlases of the
                current user level.
(5) New:        Added new surface reconstruction pipeline cat_surf_pbt3 for
                first internal tests and added test code in cat_main and
                cat_surf_createCS.
(6) Changed:    Increased number of smoothing iterations in cat_vol_pbtv.cpp.


------------------------------------------------------------------------
r1308 | gaser | 2018-04-17 16:47:58 +0200 (Tue, 17 Apr 2018) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_defaults.m
M       cat_main.m
M       html/cat.html

Fixed: FA variable was not always available in cat_main.m

------------------------------------------------------------------------
r1307 | dahnke | 2018-04-17 13:27:20 +0200 (Tue, 17 Apr 2018) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main.m
M       cat_main_registration.m
M       cat_vol_morph.m

(1) Changed:    Updated cat_vol_morph with further differentiation
                between the classical chessboard and euclidean metrics.
(2) New:        Added new Shooting-based skull-stripping for experts.
(3) Changed:    Updated verbose behavior of cat_main_registration.


------------------------------------------------------------------------
r1306 | gaser | 2018-04-16 17:33:58 +0200 (Mon, 16 Apr 2018) | 21 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_defaults.m
M       cat_main.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_surf_createCS.m
M       html/cat_starting.html
M       tbx_cfg_cat.m

(1) Changed: Extended ROI options in GUI to select single atlases.
(2) Fixed: Issues with img extension in cat_run_job.m.
(3) Changed: For images with reasonable spatial resolution (mean<1.3mm)
    the reducepatch function will be skipped and the surface with original
    (voxel) resolution will be used in cat_surf_createCS. Furthermore, the
    higher-resoluted Yppi image will be used for deforming surfaces and the
    weighting for correcting the central surface in highly folded areas with
    high mean curvature is increased to 0.3.

------------------------------------------------------------------------
r1305 | dahnke | 2018-04-13 21:01:25 +0200 (Fri, 13 Apr 2018) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_io_writenii.m
M       cat_main.m
M       cat_main_registration.m

(1) Fixed:    Correct output of iy_*.nii and dt*.nii of Shooting.


------------------------------------------------------------------------
r1304 | dahnke | 2018-04-11 10:11:38 +0200 (Wed, 11 Apr 2018) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_registration.m
M       cat_vol_imcalc.m

(1) Fixed:    Corrected atlas mapping in cat_main.
(2) Fixed:    Corrected bug in the estimation of the
              Jacobian determinant in cat_main_registration.
(3) Fixed:    Corrected data type of the output in cat_vol_imcalc.


------------------------------------------------------------------------
r1303 | dahnke | 2018-04-10 12:43:59 +0200 (Tue, 10 Apr 2018) | 7 lines

Changed paths:
M       CHANGES.txt
MM      cat_install_tfce.m
M       tbx_cfg_cat.m

(1) Fixed:    Corrected bug in tbx_cfg_cat.

------------------------------------------------------------------------
r1302 | dahnke | 2018-04-10 12:34:57 +0200 (Tue, 10 Apr 2018) | 27 lines

Changed paths:
M       CHANGES.txt
M       cat_io_writenii.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_surf_createCS.m
M       cat_vol_morph.m
M       cat_vol_resize.m
A       internal/old
M       tbx_cfg_cat.m

(1) Changed:  Added optimizations in cat_vol_morph to improve
              processing speed.
(2) Changed:  Removed old code in cat_run_joband cat_run_job1070 and
              removed the lower intensity limitation that may troubles
              the CSF/background segmentation.
(3) Fixed:    Corrected data mapping error in cat_vol_ROInorm.
(4) Fixed:    Corrected output error of iY*.nii in cat_main.
(5) Fixed:    Corrected output error of atlas maps in cat_main.
(6) Fixed:    Corrected small bug in cat_vol_resize.
(7) Fixed:    Corrected problems with the main resolution limit
              of some preprocessing steps in cat_main and cat_main_LAS.
(8) New:      Added atlas export field in expert GUI.


------------------------------------------------------------------------
r1301 | gaser | 2018-04-09 16:05:37 +0200 (Mon, 09 Apr 2018) | 27 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat12.m
A       cat_install_tfce.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_createCS.m
M       cat_surf_display.m
M       cat_update.m
M       html/cat.html
M       html/cat_starting.html
M       html/cat_versions.html
M       tbx_cfg_cat.m

(1) Changed: Disabled volume-based thickness estimation option.
(2) Fixed: Display of surfaces without color (texture) information was not
    working in cat_surf_display.m.
(3) Changed: Added estimation of pial and white matter surface and use these
    surfaces to correct cortical thickness.
(4) Changed: Added internal option to save beta images in
    cat_stat_analyze_ROIs.m
(5) Changed: Updated online help and CAT12 manual.
(6) Added: Function for installing TFCE toolbox was added and will be called
    from quick start guide if TFCE is not yet installed.

------------------------------------------------------------------------
r1300 | gaser | 2018-03-26 16:20:21 +0200 (Mon, 26 Mar 2018) | 24 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_batch_cat.m
M       cat_conf_long.m
M       cat_defaults.m
M       cat_main.m
M       cat_stat_spm.m
M       html/cat_versions.html
M       tbx_cfg_cat.m

(1) Changed: Updated version information to CAT12.3
(2) Fixed: Corrected flag for cortical thickness files and moved option
    to save these maps to developer mode.
(3) Changed: Added error message to cat_stat_spm if SPM.mat was probably not
    correctly saved because of missing "-v7.3" flag in spm_defaults.m.
(4) Changed: Increased threshold for writing thickness maps to 0.1, which is
    still not optimal because too much of thickness is defined in areas
    with low GM probability.
(5) Changed: Enabled cobra atlas for ROI analysis by default.
(6) Changed: Updated longitudinal batch to consider last changes in CAT12.3.


------------------------------------------------------------------------
r1299 | gaser | 2018-03-23 14:39:14 +0100 (Fri, 23 Mar 2018) | 20 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_main_cleanup.m
M       cat_main_gintnorm.m
M       cat_vol_morph.m
M       cat_vol_partvol.m
M       cat_vol_qa.m
M       cat_vol_sanlm.m
M       html/cat.html
M       spm_cat12.m
M       tbx_cfg_cat.m

Changed: Updated help text.

------------------------------------------------------------------------
r1298 | dahnke | 2018-03-23 12:07:51 +0100 (Fri, 23 Mar 2018) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_io_writenii.m
M       cat_main.m
M       cat_surf_createCS.m
M       tbx_cfg_cat.m

(1) New:    Added cortical thickness map export to expert GUI
            that runs the volumetric part of cat_surf_create_CS
            and create *ct*.nii files.
(2) New:    Added cortical thickness ROI estimation for standard
            users. Limit thickness atlas estimation to the GM and
            renamed the main atlas field to ct.

------------------------------------------------------------------------
r1297 | dahnke | 2018-03-22 16:23:05 +0100 (Thu, 22 Mar 2018) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_vol_div.m
M       cat_vol_grad.m
M       cat_vol_sanlm.m

(1) Changed: Modified NAN handling in cat_vol_div and cat_vol_grad.
             The replacement by the cat_vol_vbdist function create
             edges in the NAN regions. Now, only the neighborhood
             is replaced for the gradient/divergence estimation and
             the NAN region is set to zero.
(2) New:     Added option in the cat_vol_sanlm filter to garantie a
             minimal amount of noise in the images to avoid problems
             by segmentation routines that expect a little variation
             in the data.
(3) Fixed:   Corrected bugs in NAN and INF replacement in cat_vol_sanlm.

------------------------------------------------------------------------
r1296 | dahnke | 2018-03-21 12:03:15 +0100 (Wed, 21 Mar 2018) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_run_job1070.m
M       cat_run_job_APP_init1070.m
M       cat_stat_histth.m
M       cat_surf_createCS.m

(1) Fixed:   Corrected background scaling in cat_run_job_APP_init1070
             that caused problems in MT data.


------------------------------------------------------------------------
r1295 | gaser | 2018-03-20 15:44:44 +0100 (Tue, 20 Mar 2018) | 102 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_amap.mexa64
D       cat_amap.mexglx
D       cat_amap.mexw32
M       cat_amap.mexw64
M       cat_conf_nonlin_coreg.m
M       cat_conf_tools.m
M       cat_main.m
M       cat_ornlm.mexa64
D       cat_ornlm.mexglx
D       cat_ornlm.mexw32
M       cat_ornlm.mexw64
M       cat_plot_boxplot.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_sanlm.mexa64
D       cat_sanlm.mexglx
D       cat_sanlm.mexw32
M       cat_sanlm.mexw64
M       cat_stat_analyze_ROIs.m
M       cat_system.m
M       cat_vbdist.mexa64
D       cat_vbdist.mexglx
M       cat_vbdist.mexmaci64
D       cat_vbdist.mexw32
M       cat_vbdist.mexw64
M       cat_vol_downcut.mexa64
D       cat_vol_downcut.mexglx
M       cat_vol_downcut.mexmaci64
D       cat_vol_downcut.mexw32
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.mexa64
D       cat_vol_eidist.mexglx
M       cat_vol_eidist.mexmaci64
D       cat_vol_eidist.mexw32
M       cat_vol_eidist.mexw64
D       cat_vol_eikonal3.mexglx
D       cat_vol_eikonal3.mexw32
M       cat_vol_genus0.mexa64
D       cat_vol_genus0.mexglx
D       cat_vol_genus0.mexw32
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mexa64
D       cat_vol_gradient3.mexglx
M       cat_vol_gradient3.mexmaci64
D       cat_vol_gradient3.mexw32
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mexa64
D       cat_vol_interp3f.mexglx
D       cat_vol_interp3f.mexw32
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.mexa64
D       cat_vol_laplace3.mexglx
M       cat_vol_laplace3.mexmaci64
D       cat_vol_laplace3.mexw32
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mexa64
D       cat_vol_laplace3R.mexglx
M       cat_vol_laplace3R.mexmaci64
D       cat_vol_laplace3R.mexw32
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexa64
D       cat_vol_localstat.mexglx
D       cat_vol_localstat.mexw32
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexa64
D       cat_vol_median3.mexglx
D       cat_vol_median3.mexw32
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexa64
D       cat_vol_median3c.mexglx
D       cat_vol_median3c.mexw32
M       cat_vol_median3c.mexw64
M       cat_vol_pbtp.mexa64
D       cat_vol_pbtp.mexglx
D       cat_vol_pbtp.mexw32
M       cat_vol_pbtp.mexw64
M       cat_vol_sanlm.m
M       cat_vol_simgrow.mexa64
D       cat_vol_simgrow.mexglx
M       cat_vol_simgrow.mexmaci64
D       cat_vol_simgrow.mexw32
M       cat_vol_simgrow.mexw64
M       compile.m
M       html/cat.html
M       html/cat_versions.html

(1) Changed: Updated version information to CAT12.3
(2) Changed: Added SANLM filter again as very first step because the noise
    estimation and de-noising works best for non-interpolated data.
(3) Fixed: Compilation tool was sometimes indicating non-existing errors.
(4) Fixed: cat_vol_sanlm was called 2 times because of missing "return".
(5) Fixed: CAT!2 could not be called from directories with spaces under
    unix (thanks to Marco Hermesdorf for pointing to this error).
(6) Fixed: ROI analysis was not working for Cobra atlas.
(7) Changed: Changed text interpreter in cat_plot_boxplot.m

------------------------------------------------------------------------
r1294 | gaser | 2018-03-19 21:33:44 +0100 (Mon, 19 Mar 2018) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_main.m
M       cat_vbdist.c
M       cat_vol_downcut.c
M       cat_vol_eidist.c
M       cat_vol_eikonal3.c
M       cat_vol_gradient3.c
M       cat_vol_laplace3.c
M       cat_vol_laplace3R.c
M       cat_vol_pbt.m
M       cat_vol_sanlm.m
M       cat_vol_simgrow.c

Changed: Corrected uncountable number of typos.

------------------------------------------------------------------------
r1293 | dahnke | 2018-03-19 15:48:24 +0100 (Mon, 19 Mar 2018) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_vol_pbt.m

Changed:    Updated post-SPM segmentation correction after
            skull-stripping to reduce problems in data with
            thin skulls (children).

------------------------------------------------------------------------
r1292 | dahnke | 2018-03-19 10:27:06 +0100 (Mon, 19 Mar 2018) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_io_volctype.m
M       cat_run_job.m
M       cat_stat_histth.m
M       cat_vol_sanlm.m

Changed:    Updated "cat_vol_sanlm" filter and its GUI to avoid over
            filtering of low intensity areas.
New:        Added GUI for "cat_io_ctype" that convert the data type
            of images (eg. float > uint8) to save disk space.





------------------------------------------------------------------------
r1291 | dahnke | 2018-03-15 13:34:45 +0100 (Thu, 15 Mar 2018) | 23 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_histth.m
M       cat_surf_createCS.m
M       cat_surf_parameters.m
M       cat_vol_eidist.c
M       cat_vol_eidist.mexmaci64
M       cat_vol_pbt.m
M       cat_vol_pbtv.cpp
M       cat_vol_pbtv.mexmaci64

Changed:    Added defaults parameter in "cat_surf_parameters".
Changed:    Updated parameter structure in "cat_stat_histth" and
            added box and violin plots.
Changed:    Updated "cat_vol_eidist.c".
Changed:    Updated pbtv-case in "cat_vol_pbt" and added comments.
Changed:    Added smoothing step in "cat_vol_pbtv.m".






------------------------------------------------------------------------
r1290 | gaser | 2018-03-08 15:18:27 +0100 (Thu, 08 Mar 2018) | 11 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       html/cat.html
M       html/cat_starting.html
M       html/cat_versions.html

Changed: Updated CAT12 manual and online help

------------------------------------------------------------------------
r1289 | gaser | 2018-03-08 12:12:16 +0100 (Thu, 08 Mar 2018) | 60 lines

Changed paths:
M       Amap.c
M       Amap.h
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_amap.c
M       cat_amap.mexa64
M       cat_amap.mexmaci64
M       cat_amap.mexw64
M       cat_main.m
M       cat_ornlm.mexmaci64
M       cat_ornlm.mexw64
M       cat_sanlm.mexmaci64
M       cat_sanlm.mexw64
M       cat_vbdist.mexmaci64
M       cat_vbdist.mexw64
M       cat_vol_defs.m
M       cat_vol_downcut.mexa64
M       cat_vol_downcut.mexmaci64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.c
M       cat_vol_eidist.mexa64
M       cat_vol_eidist.mexmaci64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.mexa64
M       cat_vol_genus0.mexmaci64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mexa64
M       cat_vol_gradient3.mexmaci64
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mexmaci64
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.mexmaci64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mexmaci64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexa64
M       cat_vol_localstat.mexmaci64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexa64
M       cat_vol_median3.mexmaci64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexmaci64
M       cat_vol_median3c.mexw64
M       cat_vol_pbtp.mexmaci64
M       cat_vol_pbtp.mexw64
M       cat_vol_simgrow.mexa64
M       cat_vol_simgrow.mexmaci64
M       cat_vol_simgrow.mexw64
M       html/cat.html
M       vollib.c

(1) Fixed: Applying deformations to img/hdr data was not working (thanks to
    David Berro for pointing to this error).
(2) Changed: Updated size of window, fonts and buttons in cat12.m.
(3) Changed: Updated internal bias correction in Amapc.c which is still
    experimental.
(4) Changed: Canceled Roberts last changes in cat_vol_eidist.c.

------------------------------------------------------------------------
r1288 | gaser | 2018-03-06 16:28:35 +0100 (Tue, 06 Mar 2018) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       html/cat.html

Changed: Modified skull-stripping for inverted data (i.e. T2/PD).

------------------------------------------------------------------------
r1287 | gaser | 2018-03-05 16:17:42 +0100 (Mon, 05 Mar 2018) | 17 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_batch_cat.sh
M       cat_conf_extopts.m
MM      cat_spm_preproc_write8.m
MM      cat_stat_histth.m
 M      cat_vol_pbtv.cpp
 M      cat_vol_pbtv.mexmaci64
M       html/cat.html
M       html/cat_versions.html

(1) Fixed: Option "-nojvm" in cat_batch_cat.sh was not correctly working.
(2) Fixed: Corrected typos in help text.

------------------------------------------------------------------------
r1286 | gaser | 2018-03-05 12:44:37 +0100 (Mon, 05 Mar 2018) | 47 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_io_3Dto4D.m
M       cat_io_FreeSurfer.m
M       cat_io_writenii.m
M       cat_io_xml2csv.m
M       cat_main.m
M       cat_main_cleanup.m
M       cat_main_gcut.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_spm_preproc_run.m
M       cat_spm_preproc_write8.m
M       cat_stat_analyze_ROIs.m
M       cat_stat_check_cov.m
M       cat_surf_avg.m
M       cat_surf_createCS.m
M       cat_surf_resamp.m
M       cat_vol_approx.m
M       cat_vol_average.m
M       cat_vol_defs.m
M       cat_vol_pbt.m
M       cat_vol_pbtp.cpp
M       cat_vol_pbtp.mexmaci64
M       html/cat.html
M       slice_overlay.m
M       tbx_cfg_cat.m

(1) Changed: Moved options for cerebellar surface extraction to developer
    mode.
(2) Fixed: Disabled use of mask for resampling cerebellar surfaces in
    cat_surf_resample.m.
(3) Changed: Canceled Roberts changes from r1285 in cat_vol_pbt* because these
    functions have to be tested more carefully and are not yet working.
(4) Fixed: Ygm and Ywm were not defined in cat_main_gcut.m.
(5) Changed: Decreased weighting of final cleanup because it sometimes removed
    parts of the brain.
(6) Changed: Default skull-stripping is again medium gcut that is now modified
    and also uses skulltripping based on SPM12 segmentations.
(7) Fixed: Variable fname is reserved function and caused issues on deployed
    versions.
(8) Changed: Added

------------------------------------------------------------------------
r1285 | gaser | 2018-02-28 08:19:05 +0100 (Wed, 28 Feb 2018) | 24 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_registration.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1070.m
D       cat_run_oldcatch.m
M       cat_spm_preproc_run.m
A       cat_spm_preproc_write8.m
M       cat_vol_morph.m
M       cat_vol_resize.m

(1) Deleted: Removed cat_run_oldcatch.m
(2) New: cat_spm_preproc_write8.m to obtain and write SPM12 segmentations.
(3) Changed: Removed initial SANLM filtering in cat_run_job* because SPM12
    segmentation approach is more stable with noisier data esp. in CSF.
(4) Changed: Added detection of already skull-stripped data in
    cat_run_job1070.m.
(5) Changed: Default skull-stripping with gcutstr=0 now uses mask with
    threshold of 0.5.
(6) Changed: SANLM filtering in cat_main is now using whole brain.
(7) Fixed: Order of GM/WM/CSF volume estimates is now correct.

------------------------------------------------------------------------
r1284 | dahnke | 2018-02-27 16:35:12 +0100 (Tue, 27 Feb 2018) | 40 lines

Changed paths:
M       CHANGES.txt
M       cat_io_FreeSurfer.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_main_gcut.m
A       cat_stat_histth.m
M       cat_surf_createCS.m
M       cat_vol_eidist.c
M       cat_vol_morph.m
M       cat_vol_partvol.m
M       cat_vol_pbt.m
M       cat_vol_pbtp.cpp
M       cat_vol_pbtp.mexmaci64
A       cat_vol_pbtv.cpp
A       cat_vol_pbtv.mexmaci64

Fixed:    Corrected bug in "cat_morph_vol".
New:      Added "fs2cat" function in "cat_io_FreeSurfer" to import
          FreeSurfer subjects partially.
New:      Added equi-volume PBT routine "cat_vol_pbtv.cpp".
Changed:  Updated equi-distance PBT routine "cat_vol_pbtp.cpp".
Changed:  Memory optimization in "cat_main".
          Added detailed command line output of SPM preprocessing steps.
Changed:  Added general resolution limit "job.extopts.uhrlim" for
          ultrahigh-resolution data in "cat_vol_gcut", "cat_vol_partvol"
          and "cat_vol_LAS".
Changed:  Tiny changes in command line output in "cat_vol_nlmus".
Changed:  Added cleanup in "cat_vol_pbt" that is at least required for
          high-resolution data.
Changed:  Added resolution adaption depending on the resolution of
          the input image, ie high-resolution volumes will create
          high resolution surfaces.







------------------------------------------------------------------------
r1283 | gaser | 2018-02-20 11:40:00 +0100 (Tue, 20 Feb 2018) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_gcut.m
M       cat_stat_check_cov.m
 M      html/cat_versions.html

(1) Fixed: Displayed Slices for sorted variance-covariance matrix were mixed
    up in cat_stat_check_cov.m
(2) Changed: Added more CSF segmentation to brainmask in cat_main.m and
    cat_main_gcut.m

------------------------------------------------------------------------
r1282 | gaser | 2018-02-19 08:14:50 +0100 (Mon, 19 Feb 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       check_pipeline/batch_surface_pipeline.m

Fixed: Pipeline check for surfaces was not correctly working.

------------------------------------------------------------------------
r1281 | gaser | 2018-02-18 23:05:09 +0100 (Sun, 18 Feb 2018) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_max.m

Fixed: In rare cases where local maxima are not correctly found the
number of clusters differs from cluster indices in A. Then, we have
to add non-unique entries using function find_connected_component
in cat_surf_max.m.

------------------------------------------------------------------------
r1280 | gaser | 2018-02-16 17:20:12 +0100 (Fri, 16 Feb 2018) | 22 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_defaults.m
M       cat_surf_results.m
M       html/cat.html
M       html/cat.txt
M       html/cat_orthogonality.html
A       html/cat_versions.html
M       html/style.css
M       spm_cat12.m

(1) Updated: New version CAT12.2 (r1280)
(2) Changed: Added version information to CAT12 manual and interactive
    help
(3) Changed: Default skull-stripping is now using SPM12 cleanup which
    is more conservative and keeps more extracranial CSF. This results
    in more reliable TIV values, especially for atrophied brains.

------------------------------------------------------------------------
r1279 | gaser | 2018-02-15 09:46:37 +0100 (Thu, 15 Feb 2018) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_cva_ui.m
M       html/cat.html

Fixed: cat_stat_cva_ui.m was not correctly working for surfaces.

------------------------------------------------------------------------
r1278 | gaser | 2018-02-14 17:43:39 +0100 (Wed, 14 Feb 2018) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_check_cov.m
M       html/cat.html

Changed: Updated code for opaque overlay in cat_stat_check_cov.m

------------------------------------------------------------------------
r1277 | gaser | 2018-02-13 13:35:52 +0100 (Tue, 13 Feb 2018) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
MM      cat_stat_factorial_design.m
M       html/cat.html
M       html/cat.txt
M       html/cat_starting.html
M       html/style.css

Changed: Corrected css-code for "Quick Start Guide" button in CAT12 winodw.

------------------------------------------------------------------------
r1276 | gaser | 2018-02-13 10:56:53 +0100 (Tue, 13 Feb 2018) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       html/cat.html
M       html/cat.txt
M       html/style.css

Changed: Added button to open external "Quick Start Guide" to CAT12 winodw.

------------------------------------------------------------------------
r1275 | gaser | 2018-02-12 23:00:05 +0100 (Mon, 12 Feb 2018) | 28 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat12.m
M       cat_conf_tools.m
A  +    cat_stat_check_SPM.m
        > moved from cat_stat_check_cov_SPM.m
M       cat_stat_check_cov.m
D       cat_stat_check_cov_SPM.m
        > moved to cat_stat_check_SPM.m
A       cat_stat_factorial_design.m
M       html/cat.html
M       html/cat.txt
M       html/cat_methods_FN.html
M       html/cat_orthogonality.html
M       html/cat_starting.html
M       html/style.css

(1) Changed: Use smaller font in online help and added comments where to
    synchronize with CAT12 manual.
(2) Changed: Updated CAT12 manual and online help (orthogonality check)
(3) Changed: Renamed cat_stat_check_cov_SPM.m to cat_stat_check_SPM.m.
(4) Changed: Added batch mode for checking SPM design.
(5) Changed: Added check for SPM design to basic models.
(6) Changed: Many changes to cat_stat_check_SPM.m and cat_stat_check_cov.m.
(7) Changed: Added global scaling to cat_stat_check_cov.m

------------------------------------------------------------------------
r1274 | gaser | 2018-02-12 09:36:30 +0100 (Mon, 12 Feb 2018) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       html/cat.html

Fixed: cat_surf_main.m estimated completely wrong TIV and tissue volumes.



------------------------------------------------------------------------
r1273 | gaser | 2018-02-09 14:41:30 +0100 (Fri, 09 Feb 2018) | 8 lines

Changed paths:
M       CHANGES.txt
MM      cat_stat_check_cov_SPM.m
M       cat_surf_vol2surf.m

Fixed: Mapping for native volumes to surface crashed because of typo.


------------------------------------------------------------------------
r1272 | gaser | 2018-02-09 13:21:57 +0100 (Fri, 09 Feb 2018) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_check_cov.m
M       cat_stat_check_cov_SPM.m
M       html/cat.html

Changed: Added slider for transparent overlay of differences to sample
mean to cat_stat_check_vol.m.


------------------------------------------------------------------------
r1271 | gaser | 2018-02-08 15:28:51 +0100 (Thu, 08 Feb 2018) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_conf_stools.m
M       cat_stat_check_cov.m
A       cat_stat_check_cov_SPM.m
M       cat_surf_display.m
M       cat_surf_render.m
M       cat_surf_results.m

(1) Fixed: Selected filename was not used for suggesting name for saving
    image file in cat_surf_results.
(2) Fixed: Colorrange couldn't be defined if NaN#s were found in the
    colordata in cat_surf_render.m.
(3) Changed: Added function to check sample homogeneity defined in an
    existing SPM.mat design.


------------------------------------------------------------------------
r1270 | gaser | 2018-02-07 14:32:14 +0100 (Wed, 07 Feb 2018) | 25 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_cat.m
M       cat_batch_cat.sh
M       cat_batch_long.m
M       cat_batch_long.sh
M       cat_batch_spm.sh
M       cat_conf_tools.m
M       cat_main.m
M       cat_run_newcatch.m
M       cat_run_oldcatch.m
M       cat_surf_info.m
D       cat_tst_qa.m
        > moved to cat_vol_qa.m
A  +    cat_vol_qa.m
        > moved from cat_tst_qa.m

(1) Fixed: cat_surf_info now also gives correct Pmesh if data are called
    on a different computer and SPM12 folder changed.
(2) Changed: TIV is now estimated straightforward using sum of (native)
    tissue class.
(3) Changed: Renamed cat_tst_qa.m to cat_vol_qa.m
(4) Changed: Updated batch functions to be more consistent and added many
    new flags.

------------------------------------------------------------------------
r1269 | gaser | 2018-02-02 17:46:12 +0100 (Fri, 02 Feb 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_cat.sh

Changed: Added optional nojvm flag to cat_batch_cat.sh.

------------------------------------------------------------------------
r1268 | gaser | 2018-02-02 17:26:17 +0100 (Fri, 02 Feb 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_cat.sh

Fixed: used wrong flag in cat_batch_cat.sh.

------------------------------------------------------------------------
r1267 | gaser | 2018-02-02 15:47:02 +0100 (Fri, 02 Feb 2018) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_check_cov.m
M       html/cat.html

Fixed: Surface maps for Mahalanobis plot were shifted.

------------------------------------------------------------------------
r1266 | gaser | 2018-02-01 11:58:29 +0100 (Thu, 01 Feb 2018) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_analyze_ROIs.m
M       html/cat.html
M       internal/cat_vol_cMRegularizarNLM3D.mexmaci64

Fixed: Typo in cat_stat_analyze_ROIs.m that caused crash.

------------------------------------------------------------------------
r1265 | gaser | 2018-02-01 11:10:55 +0100 (Thu, 01 Feb 2018) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_stat_analyze_ROIs.m
M       cat_vol_morph.m
M       cat_vol_sanlm.m

(1) Changed: Replaced spm_con_vol by convn in cat_vol_morph which is faster and
    less memory demanding.
(2) Changed: Updated some help texts.


------------------------------------------------------------------------
r1264 | gaser | 2018-01-30 12:02:00 +0100 (Tue, 30 Jan 2018) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_resamp_freesurfer.m

Fixed: Error in last change of cat_surf_resamp_freesurfer.m with other
parameters than thickness.


------------------------------------------------------------------------
r1263 | gaser | 2018-01-30 11:56:31 +0100 (Tue, 30 Jan 2018) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_surf_resamp_freesurfer.m

(1) Fixed: Resampling of Freesurfer data was not working with new 32k mesh
    option.
(2) Changed: Added option to also resample other Freesurfer measures.

------------------------------------------------------------------------
r1262 | gaser | 2018-01-30 11:27:34 +0100 (Tue, 30 Jan 2018) | 42 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
 M      atlases_surfaces/atlases_surfaces.man
 M      atlases_surfaces_32k/atlases_surfaces_32k.man
 M      atlases_surfaces_32k/lh.Schaefer2018_1000Parcels_17Networks_order.annot
 M      atlases_surfaces_32k/lh.Schaefer2018_1000Parcels_7Networks_order.annot
 M      atlases_surfaces_32k/lh.Schaefer2018_100Parcels_17Networks_order.annot
 M      atlases_surfaces_32k/lh.Schaefer2018_100Parcels_7Networks_order.annot
 M      atlases_surfaces_32k/lh.Schaefer2018_200Parcels_17Networks_order.annot
 M      atlases_surfaces_32k/lh.Schaefer2018_200Parcels_7Networks_order.annot
 M      atlases_surfaces_32k/lh.Schaefer2018_400Parcels_17Networks_order.annot
 M      atlases_surfaces_32k/lh.Schaefer2018_400Parcels_7Networks_order.annot
 M      atlases_surfaces_32k/lh.Schaefer2018_600Parcels_17Networks_order.annot
 M      atlases_surfaces_32k/lh.Schaefer2018_600Parcels_7Networks_order.annot
 M      atlases_surfaces_32k/lh.Schaefer2018_800Parcels_17Networks_order.annot
 M      atlases_surfaces_32k/lh.Schaefer2018_800Parcels_7Networks_order.annot
 M      atlases_surfaces_32k/rh.Schaefer2018_1000Parcels_17Networks_order.annot
 M      atlases_surfaces_32k/rh.Schaefer2018_1000Parcels_7Networks_order.annot
 M      atlases_surfaces_32k/rh.Schaefer2018_100Parcels_17Networks_order.annot
 M      atlases_surfaces_32k/rh.Schaefer2018_100Parcels_7Networks_order.annot
 M      atlases_surfaces_32k/rh.Schaefer2018_200Parcels_17Networks_order.annot
 M      atlases_surfaces_32k/rh.Schaefer2018_200Parcels_7Networks_order.annot
 M      atlases_surfaces_32k/rh.Schaefer2018_400Parcels_17Networks_order.annot
 M      atlases_surfaces_32k/rh.Schaefer2018_400Parcels_7Networks_order.annot
 M      atlases_surfaces_32k/rh.Schaefer2018_600Parcels_17Networks_order.annot
 M      atlases_surfaces_32k/rh.Schaefer2018_600Parcels_7Networks_order.annot
 M      atlases_surfaces_32k/rh.Schaefer2018_800Parcels_17Networks_order.annot
 M      atlases_surfaces_32k/rh.Schaefer2018_800Parcels_7Networks_order.annot
M       cat_conf_stools.m
M       cat_surf_info.m
M       cat_surf_vol2surf.m
M       html/cat.html
 M      templates_1.50mm/templates.man

(1) Fixed: cat_surf_info had difficulties with sqrtsulc data.
(2) Changed: Added output of mapping parameters in cat_surf_vol2surf.m.
(3) Changed: Updated CAT12 manual and online help.


------------------------------------------------------------------------
r1261 | gaser | 2018-01-29 15:33:03 +0100 (Mon, 29 Jan 2018) | 17 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_surf_vol2surf.m
M       check_pipeline/batch_surface_pipeline.m
M       check_pipeline/batch_volume_pipeline.m
M       html/cat_FAQ.html
M       html/cat_instruction_templates.html
M       html/cat_methods_VBM.html
M       templates_1.50mm/templates.man

(1) Changed: Updated pipeline check.
(2) Changed: Added output of mapping parameters in cat_surf_vol2surf.m.
(3) Chnaged: Updated CAT12 manual and online help.

------------------------------------------------------------------------
r1260 | gaser | 2018-01-26 20:15:00 +0100 (Fri, 26 Jan 2018) | 47 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
D       atlases_surfaces/a2005s.txt
D       atlases_surfaces/a2009s.txt
A       atlases_surfaces/atlases_surfaces.man
A       atlases_surfaces_32k/atlases_surfaces_32k.man
A       atlases_surfaces_32k/lh.Schaefer2018_1000Parcels_17Networks_order.annot
A       atlases_surfaces_32k/lh.Schaefer2018_1000Parcels_7Networks_order.annot
A       atlases_surfaces_32k/lh.Schaefer2018_100Parcels_17Networks_order.annot
A       atlases_surfaces_32k/lh.Schaefer2018_100Parcels_7Networks_order.annot
A       atlases_surfaces_32k/lh.Schaefer2018_200Parcels_17Networks_order.annot
A       atlases_surfaces_32k/lh.Schaefer2018_200Parcels_7Networks_order.annot
A       atlases_surfaces_32k/lh.Schaefer2018_400Parcels_17Networks_order.annot
A       atlases_surfaces_32k/lh.Schaefer2018_400Parcels_7Networks_order.annot
A       atlases_surfaces_32k/lh.Schaefer2018_600Parcels_17Networks_order.annot
A       atlases_surfaces_32k/lh.Schaefer2018_600Parcels_7Networks_order.annot
A       atlases_surfaces_32k/lh.Schaefer2018_800Parcels_17Networks_order.annot
A       atlases_surfaces_32k/lh.Schaefer2018_800Parcels_7Networks_order.annot
A       atlases_surfaces_32k/rh.Schaefer2018_1000Parcels_17Networks_order.annot
A       atlases_surfaces_32k/rh.Schaefer2018_1000Parcels_7Networks_order.annot
A       atlases_surfaces_32k/rh.Schaefer2018_100Parcels_17Networks_order.annot
A       atlases_surfaces_32k/rh.Schaefer2018_100Parcels_7Networks_order.annot
A       atlases_surfaces_32k/rh.Schaefer2018_200Parcels_17Networks_order.annot
A       atlases_surfaces_32k/rh.Schaefer2018_200Parcels_7Networks_order.annot
A       atlases_surfaces_32k/rh.Schaefer2018_400Parcels_17Networks_order.annot
A       atlases_surfaces_32k/rh.Schaefer2018_400Parcels_7Networks_order.annot
A       atlases_surfaces_32k/rh.Schaefer2018_600Parcels_17Networks_order.annot
A       atlases_surfaces_32k/rh.Schaefer2018_600Parcels_7Networks_order.annot
A       atlases_surfaces_32k/rh.Schaefer2018_800Parcels_17Networks_order.annot
A       atlases_surfaces_32k/rh.Schaefer2018_800Parcels_7Networks_order.annot
M       cat_conf_stools.m
M       cat_roi_fun.m
M       cat_stat_check_cov.m
M       cat_surf_display.m
M       cat_surf_vol2surf.m
M       compile.m
M       html/cat_starting.html
A       templates_1.50mm/templates.man

(1) Changed: Updated CAT12 manual and online help.
(2) Changed: Added equi-volume model by Bok and multi-save option to
    cat_surf_vol2surf.m.
(3) Fixed: Bug with label files where filenames were not used in the title.
(4) Added: New description of templates.

------------------------------------------------------------------------
r1259 | gaser | 2018-01-24 08:53:21 +0100 (Wed, 24 Jan 2018) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
D       cat12.fig
M       cat12.m
M       cat_surf_display.m
M       html/cat.html

(1) Fixed: Issues with missing colordata in cat_surf_display.m
(2) Changed: cat12 figure is now only based on cat12.m and no cat12.fig is
    needed anymore. This helps to get rid of issues with different Matlab
    versions and Guide.

------------------------------------------------------------------------
r1258 | gaser | 2018-01-22 17:58:03 +0100 (Mon, 22 Jan 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat12.fig
M       cat_vol_morph.m

Fixed: cat12.fig could not be loaded with older matlab versions.

------------------------------------------------------------------------
r1257 | gaser | 2018-01-19 17:03:11 +0100 (Fri, 19 Jan 2018) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_roi_fun.m
M       cat_surf_createCS.m
M       html/cat.html

(1) Changed: Estimation of mean ROI values now skips some of unnecessary values.
(2) Changed: Added final correction of central surface in highly folded areas
    with high mean curvature.

------------------------------------------------------------------------
r1256 | gaser | 2018-01-17 23:18:05 +0100 (Wed, 17 Jan 2018) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_vol2surf.m
M       check_pipeline/mri/mwp1IXI002-Guys-0828-T1.nii
M       check_pipeline/report/cat_IXI002-Guys-0828-T1.mat
M       check_pipeline/report/cat_IXI002-Guys-0828-T1.xml

Fixed: cat_surf_vol2surf.m is now also working if only the left hemisphere
files exist.

------------------------------------------------------------------------
r1255 | gaser | 2018-01-12 09:08:18 +0100 (Fri, 12 Jan 2018) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       html/cat.html

(1) Fixed: Mapping of native volumes with very high resolution (<0.6mm) to
    native surfaces was not working on some computers.

------------------------------------------------------------------------
r1254 | gaser | 2018-01-10 16:41:43 +0100 (Wed, 10 Jan 2018) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_main.m
M       cat_surf_vol2surf.m
M       html/cat.html

(1) Fixed: Issue with missing hemi_merge flag for native volume to surface
    mapping.
(2) Fixed: Native written atlases used wrong deformation fields.

------------------------------------------------------------------------
r1253 | gaser | 2018-01-10 12:23:35 +0100 (Wed, 10 Jan 2018) | 17 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat12.fig
M       html/cat.html
M       html/cat.txt
M       html/cat_methods.html
M       html/cat_methods_FN.html
M       html/cat_methods_MS.html
M       html/style.css
 M      templates_surfaces_32k/lh.thickness.Template_T1_IXI555_MNI152_GS
 M      templates_surfaces_32k/rh.thickness.Template_T1_IXI555_MNI152_GS

Changed: Updated interactive help and manual.

------------------------------------------------------------------------
r1252 | gaser | 2018-01-10 10:29:11 +0100 (Wed, 10 Jan 2018) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_surf_display.m
M       cat_surf_info.m
M       cat_surf_rename.m
M       cat_surf_vol2surf.m
M       html/cat.html

(1) Fixed: Mapping of normalized volumes to template surface had issues with
    file renaming.
(2) Changed: Updated some help texts.
(3) Fixed: Rendering issues for data with small values in cat_surf_display.

------------------------------------------------------------------------
r1251 | gaser | 2017-12-29 10:22:44 +0100 (Fri, 29 Dec 2017) | 17 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_surf_resamp.m
M       cat_surf_vol2surf.m
M       html/cat.html
M       html/cat_starting.html
A       templates_surfaces_32k/lh.thickness.Template_T1_IXI555_MNI152_GS
A       templates_surfaces_32k/rh.thickness.Template_T1_IXI555_MNI152_GS

(1) Fixed: Added options for 32k meshes and merging hemispheres to mapping
function for normalized volumes to template surface.
(2) Changed: Cleaning field names in cat_conf_stools.m

------------------------------------------------------------------------
r1250 | gaser | 2017-12-20 17:17:28 +0100 (Wed, 20 Dec 2017) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Contents_info.txt
M       Makefile
M       cat_run_job1070.m
M       cat_surf_render2.m
M       cat_version.m
M       html/cat.html
M       html/cat.txt
M       spm_cat12.m

Changed: New stable CAT12 version is called CAT12.1. All following
updates till version 12.2 should not affect preprocessing of the data.

------------------------------------------------------------------------
r1249 | gaser | 2017-12-15 14:54:56 +0100 (Fri, 15 Dec 2017) | 21 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_surf_resamp.m
M       html/cat.html
M       html/cat_starting.html
 M      templates_animals/chimpanzee_T1.nii
 M      templates_animals/chimpanzee_TPM.nii
 M      templates_animals/chimpanzee_Template_0_GS.nii
 M      templates_animals/chimpanzee_Template_1_GS.nii
 M      templates_animals/chimpanzee_Template_2_GS.nii
 M      templates_animals/chimpanzee_Template_3_GS.nii
 M      templates_animals/chimpanzee_Template_4_GS.nii
 M      templates_animals/chimpanzee_brainmask.nii

Changed: Recommendation for surface smoothing is again 15mm even for the new
smoothing method. Changed all links to this new value.

------------------------------------------------------------------------
r1248 | gaser | 2017-12-15 13:06:59 +0100 (Fri, 15 Dec 2017) | 27 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
M       check_pipeline/batch_surface_pipeline.m
M       html/cat.html
M       html/cat_starting.html

(1) Fixed: Heat kernel smoothing was resolution dependent. Solved that issue
    and additionally replaced the weighting for filtering meshes with equal
    weighting. Sigma is now the mean point distance. For cortical thickness
    a good starting value is now 12-15mm, while other surface parameters
    based on cortex folding (e.g. gyrification, cortical complexity) need a
    larger filter size of about 20-25mm. Please update your scripts
    and replace the old field "fwhm" by "fwhm_surf" and adapt the values.
(1) Changed: Again added option for 32k meshes because smoothing size
    is not correct for these meshes.
(2) Changed: Added warning if old scripts with "fwhm" filed are used in
    cat_surf_resamp.m.
(3) Changed: The new name for resampled and smoothed surface data is not
    containing "mm" anymore to indicate the filter size. This is also thought
    to not mix data smoothed with the old and new smoothing method.

------------------------------------------------------------------------
r1247 | gaser | 2017-12-13 20:48:18 +0100 (Wed, 13 Dec 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_plot_boxplot.m

Fixed: Violin plot crashed if sample sizes differed in cat_plot_boxplot.m

------------------------------------------------------------------------
r1246 | dahnke | 2017-12-12 12:11:58 +0100 (Tue, 12 Dec 2017) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m

Update:   Added exptopts.print variable to expert and developer GUI and added
          a separat mode to print only values and volume data and no surfaces
          due to printing problems on server that hang-up without error.


------------------------------------------------------------------------
r1245 | dahnke | 2017-12-12 11:35:00 +0100 (Tue, 12 Dec 2017) | 24 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_main.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_vol_urqio.m
M       spm_cat12.m
M       tbx_cfg_cat.m
A       templates_animals/chimpanzee_T1.nii
A       templates_animals/chimpanzee_TPM.nii
A       templates_animals/chimpanzee_Template_0_GS.nii
A       templates_animals/chimpanzee_Template_1_GS.nii
A       templates_animals/chimpanzee_Template_2_GS.nii
A       templates_animals/chimpanzee_Template_3_GS.nii
A       templates_animals/chimpanzee_Template_4_GS.nii
A       templates_animals/chimpanzee_brainmask.nii

Update:   Added chimpanzee templates and adapted cat12 and cat_run.
Fixed:    Removed focus on Dartel template to allow ROI analysis with Shooting.
Fixed:    Corrected setting of SPM and CAT defaults in parallel processing.


------------------------------------------------------------------------
r1244 | gaser | 2017-12-12 00:33:37 +0100 (Tue, 12 Dec 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m

Fixed: Change between 32k and 164k meshes was not correct in cat_surf_results.m

------------------------------------------------------------------------
r1243 | gaser | 2017-12-11 14:02:20 +0100 (Mon, 11 Dec 2017) | 13 lines

Changed paths:
M       CHANGES.txt
 M      MBeautify.m
 M      MBeautify.txt
 M      MFormatter.m
M       cat_conf_stools.m
 M      resources/settings/MBeautyConfigurationRules.m
 M      resources/settings/MBeautyConfigurationRules.xml

(1) Changed: Temporarily removed option for 32k meshes because smoothing size
    is not correct for these meshes.
(2) Fixed: Some incorrect && checks for non-logical variables.

------------------------------------------------------------------------
r1242 | gaser | 2017-12-11 14:01:14 +0100 (Mon, 11 Dec 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_resamp.m
M       cat_surf_results.m

(1) Changed: Temporarily removed option for 32k meshes because smoothing size
    is not correct for these meshes.
(2) Fixed: Some incorrect && checks for non-logical variables.

------------------------------------------------------------------------
r1241 | gaser | 2017-12-11 00:03:26 +0100 (Mon, 11 Dec 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m

Changed: Formatted cat_surf_results.m

------------------------------------------------------------------------
r1240 | dahnke | 2017-12-07 15:52:10 +0100 (Thu, 07 Dec 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_vol_urqio.m
M       html/images/cat_tst_seg_bwp_ana.png

Fixed:  Corrected bug in CAT processing of a given SPM segmentation in cat_main.
Fixed:  Corrected errors in high-resolution preprocessing pipeline cat_vol_urqio.

------------------------------------------------------------------------
r1239 | gaser | 2017-12-07 15:04:40 +0100 (Thu, 07 Dec 2017) | 17 lines

Changed paths:
M       CHANGES.txt
A       MBeautify.m
A       MBeautify.txt
A       MFormatter.m
MM      cat_stat_spm.m
M       cat_vol_slice_overlay.m
A       resources
A       resources/settings
A       resources/settings/MBeautyConfigurationRules.m
A       resources/settings/MBeautyConfigurationRules.xml

(1) Added: Code formatting tool MBeautify that can be called inside matlab
    editor.See MBeautify.txt for more information.
(2) Changed: Tried MBeautify for cat_vol_slice_overlay and additionally
    changed interpolation to nearest neighbor.

------------------------------------------------------------------------
r1238 | gaser | 2017-12-07 11:37:48 +0100 (Thu, 07 Dec 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_plot_boxplot.m
M       html/cat.html

Changed: Replaced ksdensity function which requires statistics toolbox with
kde in cat_plot_boxplot.m to allow violin plot without external toolbox.

------------------------------------------------------------------------
r1237 | gaser | 2017-12-06 23:39:20 +0100 (Wed, 06 Dec 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m

Changed: Cleaned up cat_conf_stool.m slightly.

------------------------------------------------------------------------
r1236 | gaser | 2017-12-04 14:39:54 +0100 (Mon, 04 Dec 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
A       cat_stat_spm.m
M       html/cat_starting.html

Changed: Use workaround to deal with SPM.mat inisde cat12 now as external
function cat_stat_spm.m.

------------------------------------------------------------------------
r1235 | gaser | 2017-12-04 12:47:48 +0100 (Mon, 04 Dec 2017) | 230 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_analyze_ROIs.m
 M      check_pipeline/IXI002-Guys-0828-T1.nii
 M      check_pipeline/analysis/surface/RPV.dat
 M      check_pipeline/analysis/surface/RPV.gii
 M      check_pipeline/analysis/surface/SPM.mat
 M      check_pipeline/analysis/surface/spmF_0001.dat
 M      check_pipeline/analysis/surface/spmF_0001.gii
 M      check_pipeline/analysis/surface/spmT_0002.dat
 M      check_pipeline/analysis/surface/spmT_0002.gii
 M      check_pipeline/analysis/volume/RPV.nii
 M      check_pipeline/analysis/volume/SPM.mat
 M      check_pipeline/analysis/volume/spmF_0001.nii
 M      check_pipeline/analysis/volume/spmT_0002.nii
 M      check_pipeline/batch_surface_pipeline.m
 M      check_pipeline/batch_volume_pipeline.m
D       check_pipeline/label
        > moved to check_pipeline/label_orig
D       check_pipeline/label/catROI_IXI002-Guys-0828-T1.mat
D       check_pipeline/label/catROI_IXI002-Guys-0828-T1.xml
D       check_pipeline/label/catROI_IXI016-Guys-0697-T1.mat
D       check_pipeline/label/catROI_IXI016-Guys-0697-T1.xml
D       check_pipeline/label/catROI_IXI017-Guys-0698-T1.mat
D       check_pipeline/label/catROI_IXI017-Guys-0698-T1.xml
D       check_pipeline/label/catROI_IXI019-Guys-0702-T1.mat
D       check_pipeline/label/catROI_IXI019-Guys-0702-T1.xml
D       check_pipeline/label/catROI_IXI020-Guys-0700-T1.mat
D       check_pipeline/label/catROI_IXI020-Guys-0700-T1.xml
D       check_pipeline/label/catROI_IXI021-Guys-0703-T1.mat
D       check_pipeline/label/catROI_IXI021-Guys-0703-T1.xml
D       check_pipeline/label/catROI_IXI022-Guys-0701-T1.mat
D       check_pipeline/label/catROI_IXI022-Guys-0701-T1.xml
D       check_pipeline/label/catROI_IXI023-Guys-0699-T1.mat
D       check_pipeline/label/catROI_IXI023-Guys-0699-T1.xml
D       check_pipeline/label/catROI_IXI024-Guys-0705-T1.mat
D       check_pipeline/label/catROI_IXI024-Guys-0705-T1.xml
D       check_pipeline/label/catROI_IXI025-Guys-0852-T1.mat
D       check_pipeline/label/catROI_IXI025-Guys-0852-T1.xml
D       check_pipeline/label/catROI_IXI026-Guys-0696-T1.mat
D       check_pipeline/label/catROI_IXI026-Guys-0696-T1.xml
D       check_pipeline/label/catROI_IXI027-Guys-0710-T1.mat
D       check_pipeline/label/catROI_IXI027-Guys-0710-T1.xml
D       check_pipeline/label/catROI_IXI028-Guys-1038-T1.mat
D       check_pipeline/label/catROI_IXI028-Guys-1038-T1.xml
D       check_pipeline/label/catROI_IXI029-Guys-0829-T1.mat
D       check_pipeline/label/catROI_IXI029-Guys-0829-T1.xml
D       check_pipeline/label/catROI_IXI030-Guys-0708-T1.mat
D       check_pipeline/label/catROI_IXI030-Guys-0708-T1.xml
D       check_pipeline/label/catROI_IXI031-Guys-0797-T1.mat
D       check_pipeline/label/catROI_IXI031-Guys-0797-T1.xml
D       check_pipeline/label/catROI_IXI036-Guys-0736-T1.mat
D       check_pipeline/label/catROI_IXI036-Guys-0736-T1.xml
D       check_pipeline/label/catROI_IXI037-Guys-0704-T1.mat
D       check_pipeline/label/catROI_IXI037-Guys-0704-T1.xml
D       check_pipeline/label/catROI_IXI038-Guys-0729-T1.mat
D       check_pipeline/label/catROI_IXI038-Guys-0729-T1.xml
D       check_pipeline/label/catROI_IXI040-Guys-0724-T1.mat
D       check_pipeline/label/catROI_IXI040-Guys-0724-T1.xml
D       check_pipeline/label/catROIs_IXI002-Guys-0828-T1.mat
D       check_pipeline/label/catROIs_IXI002-Guys-0828-T1.xml
D       check_pipeline/label/catROIs_IXI016-Guys-0697-T1.mat
D       check_pipeline/label/catROIs_IXI016-Guys-0697-T1.xml
D       check_pipeline/label/catROIs_IXI017-Guys-0698-T1.mat
D       check_pipeline/label/catROIs_IXI017-Guys-0698-T1.xml
D       check_pipeline/label/catROIs_IXI019-Guys-0702-T1.mat
D       check_pipeline/label/catROIs_IXI019-Guys-0702-T1.xml
D       check_pipeline/label/catROIs_IXI020-Guys-0700-T1.mat
D       check_pipeline/label/catROIs_IXI020-Guys-0700-T1.xml
D       check_pipeline/label/catROIs_IXI021-Guys-0703-T1.mat
D       check_pipeline/label/catROIs_IXI021-Guys-0703-T1.xml
D       check_pipeline/label/catROIs_IXI022-Guys-0701-T1.mat
D       check_pipeline/label/catROIs_IXI022-Guys-0701-T1.xml
D       check_pipeline/label/catROIs_IXI023-Guys-0699-T1.mat
D       check_pipeline/label/catROIs_IXI023-Guys-0699-T1.xml
D       check_pipeline/label/catROIs_IXI024-Guys-0705-T1.mat
D       check_pipeline/label/catROIs_IXI024-Guys-0705-T1.xml
D       check_pipeline/label/catROIs_IXI025-Guys-0852-T1.mat
D       check_pipeline/label/catROIs_IXI025-Guys-0852-T1.xml
D       check_pipeline/label/catROIs_IXI026-Guys-0696-T1.mat
D       check_pipeline/label/catROIs_IXI026-Guys-0696-T1.xml
D       check_pipeline/label/catROIs_IXI027-Guys-0710-T1.mat
D       check_pipeline/label/catROIs_IXI027-Guys-0710-T1.xml
D       check_pipeline/label/catROIs_IXI028-Guys-1038-T1.mat
D       check_pipeline/label/catROIs_IXI028-Guys-1038-T1.xml
D       check_pipeline/label/catROIs_IXI029-Guys-0829-T1.mat
D       check_pipeline/label/catROIs_IXI029-Guys-0829-T1.xml
D       check_pipeline/label/catROIs_IXI030-Guys-0708-T1.mat
D       check_pipeline/label/catROIs_IXI030-Guys-0708-T1.xml
D       check_pipeline/label/catROIs_IXI031-Guys-0797-T1.mat
D       check_pipeline/label/catROIs_IXI031-Guys-0797-T1.xml
D       check_pipeline/label/catROIs_IXI036-Guys-0736-T1.mat
D       check_pipeline/label/catROIs_IXI036-Guys-0736-T1.xml
D       check_pipeline/label/catROIs_IXI037-Guys-0704-T1.mat
D       check_pipeline/label/catROIs_IXI037-Guys-0704-T1.xml
D       check_pipeline/label/catROIs_IXI038-Guys-0729-T1.mat
D       check_pipeline/label/catROIs_IXI038-Guys-0729-T1.xml
D       check_pipeline/label/catROIs_IXI040-Guys-0724-T1.mat
D       check_pipeline/label/catROIs_IXI040-Guys-0724-T1.xml
A  +    check_pipeline/label_orig
        > moved from check_pipeline/label
MM +    check_pipeline/label_orig/catROI_IXI002-Guys-0828-T1.mat
MM +    check_pipeline/label_orig/catROI_IXI002-Guys-0828-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI016-Guys-0697-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI016-Guys-0697-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI017-Guys-0698-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI017-Guys-0698-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI019-Guys-0702-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI019-Guys-0702-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI020-Guys-0700-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI020-Guys-0700-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI021-Guys-0703-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI021-Guys-0703-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI022-Guys-0701-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI022-Guys-0701-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI023-Guys-0699-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI023-Guys-0699-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI024-Guys-0705-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI024-Guys-0705-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI025-Guys-0852-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI025-Guys-0852-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI026-Guys-0696-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI026-Guys-0696-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI027-Guys-0710-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI027-Guys-0710-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI028-Guys-1038-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI028-Guys-1038-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI029-Guys-0829-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI029-Guys-0829-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI030-Guys-0708-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI030-Guys-0708-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI031-Guys-0797-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI031-Guys-0797-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI036-Guys-0736-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI036-Guys-0736-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI037-Guys-0704-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI037-Guys-0704-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI038-Guys-0729-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI038-Guys-0729-T1.xml
 M +    check_pipeline/label_orig/catROI_IXI040-Guys-0724-T1.mat
 M +    check_pipeline/label_orig/catROI_IXI040-Guys-0724-T1.xml
MM +    check_pipeline/label_orig/catROIs_IXI002-Guys-0828-T1.mat
MM +    check_pipeline/label_orig/catROIs_IXI002-Guys-0828-T1.xml
MM +    check_pipeline/label_orig/catROIs_IXI016-Guys-0697-T1.mat
MM +    check_pipeline/label_orig/catROIs_IXI016-Guys-0697-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI017-Guys-0698-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI017-Guys-0698-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI019-Guys-0702-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI019-Guys-0702-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI020-Guys-0700-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI020-Guys-0700-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI021-Guys-0703-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI021-Guys-0703-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI022-Guys-0701-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI022-Guys-0701-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI023-Guys-0699-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI023-Guys-0699-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI024-Guys-0705-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI024-Guys-0705-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI025-Guys-0852-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI025-Guys-0852-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI026-Guys-0696-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI026-Guys-0696-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI027-Guys-0710-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI027-Guys-0710-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI028-Guys-1038-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI028-Guys-1038-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI029-Guys-0829-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI029-Guys-0829-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI030-Guys-0708-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI030-Guys-0708-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI031-Guys-0797-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI031-Guys-0797-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI036-Guys-0736-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI036-Guys-0736-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI037-Guys-0704-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI037-Guys-0704-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI038-Guys-0729-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI038-Guys-0729-T1.xml
 M +    check_pipeline/label_orig/catROIs_IXI040-Guys-0724-T1.mat
 M +    check_pipeline/label_orig/catROIs_IXI040-Guys-0724-T1.xml
 M      check_pipeline/mri/mwp1IXI002-Guys-0828-T1.nii
 M      check_pipeline/mri/mwp1IXI016-Guys-0697-T1.nii
 M      check_pipeline/mri/mwp1IXI017-Guys-0698-T1.nii
 M      check_pipeline/mri/mwp1IXI019-Guys-0702-T1.nii
 M      check_pipeline/report/cat_IXI002-Guys-0828-T1.mat
 M      check_pipeline/report/cat_IXI002-Guys-0828-T1.xml
 M      check_pipeline/report/cat_IXI016-Guys-0697-T1.mat
 M      check_pipeline/report/cat_IXI016-Guys-0697-T1.xml
 M      check_pipeline/report/cat_IXI017-Guys-0698-T1.mat
 M      check_pipeline/report/cat_IXI017-Guys-0698-T1.xml
 M      check_pipeline/report/cat_IXI019-Guys-0702-T1.mat
 M      check_pipeline/report/cat_IXI019-Guys-0702-T1.xml
 M      check_pipeline/surf/lh.central.IXI002-Guys-0828-T1.gii
 M      check_pipeline/surf/lh.central.IXI016-Guys-0697-T1.gii
 M      check_pipeline/surf/lh.central.IXI017-Guys-0698-T1.gii
 M      check_pipeline/surf/lh.central.IXI019-Guys-0702-T1.gii
 M      check_pipeline/surf/lh.sphere.IXI002-Guys-0828-T1.gii
 M      check_pipeline/surf/lh.sphere.IXI016-Guys-0697-T1.gii
 M      check_pipeline/surf/lh.sphere.IXI017-Guys-0698-T1.gii
 M      check_pipeline/surf/lh.sphere.IXI019-Guys-0702-T1.gii
 M      check_pipeline/surf/lh.sphere.reg.IXI002-Guys-0828-T1.gii
 M      check_pipeline/surf/lh.sphere.reg.IXI016-Guys-0697-T1.gii
 M      check_pipeline/surf/lh.sphere.reg.IXI017-Guys-0698-T1.gii
 M      check_pipeline/surf/lh.sphere.reg.IXI019-Guys-0702-T1.gii
 M      check_pipeline/surf/lh.thickness.IXI002-Guys-0828-T1
 M      check_pipeline/surf/lh.thickness.IXI016-Guys-0697-T1
 M      check_pipeline/surf/lh.thickness.IXI017-Guys-0698-T1
 M      check_pipeline/surf/lh.thickness.IXI019-Guys-0702-T1
 M      check_pipeline/surf/rh.central.IXI002-Guys-0828-T1.gii
 M      check_pipeline/surf/rh.central.IXI016-Guys-0697-T1.gii
 M      check_pipeline/surf/rh.central.IXI017-Guys-0698-T1.gii
 M      check_pipeline/surf/rh.central.IXI019-Guys-0702-T1.gii
 M      check_pipeline/surf/rh.sphere.IXI002-Guys-0828-T1.gii
 M      check_pipeline/surf/rh.sphere.IXI016-Guys-0697-T1.gii
 M      check_pipeline/surf/rh.sphere.IXI017-Guys-0698-T1.gii
 M      check_pipeline/surf/rh.sphere.IXI019-Guys-0702-T1.gii
 M      check_pipeline/surf/rh.sphere.reg.IXI002-Guys-0828-T1.gii
 M      check_pipeline/surf/rh.sphere.reg.IXI016-Guys-0697-T1.gii
 M      check_pipeline/surf/rh.sphere.reg.IXI017-Guys-0698-T1.gii
 M      check_pipeline/surf/rh.sphere.reg.IXI019-Guys-0702-T1.gii
 M      check_pipeline/surf/rh.thickness.IXI002-Guys-0828-T1
 M      check_pipeline/surf/rh.thickness.IXI016-Guys-0697-T1
 M      check_pipeline/surf/rh.thickness.IXI017-Guys-0698-T1
 M      check_pipeline/surf/rh.thickness.IXI019-Guys-0702-T1

(1) Changed: if no results are found in cat_stat_analyze_ROIs.m then the
    option for displaying results is set to "0".
(2) Changed: Renamed label folder in check_pipeline.

------------------------------------------------------------------------
r1234 | gaser | 2017-12-04 11:52:18 +0100 (Mon, 04 Dec 2017) | 30 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_tools.m
M       cat_plot_boxplot.m
M       cat_stat_TIV.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_results.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_ui.m
M       check_pipeline/batch_surface_pipeline.m
M       check_pipeline/batch_volume_pipeline.m
M       check_pipeline/label/catROIs_IXI002-Guys-0828-T1.mat
M       check_pipeline/label/catROIs_IXI002-Guys-0828-T1.xml
M       check_pipeline/label/catROIs_IXI016-Guys-0697-T1.mat
M       check_pipeline/label/catROIs_IXI016-Guys-0697-T1.xml
M       check_pipeline/mri/mwp1IXI002-Guys-0828-T1.nii
!       check_pipeline/report/cat_IXI002-Guys-0828-T1.xml
M       html/cat.html

(1) Changed: cat_vol_slice_overlay now allows definition of xy-yorder and
    saved image.
(2) Changed: Size of slider in cat_surf_results was decreased.
(3) Changed: In cat_stat_analyze_ROIs it is now checked whether all measures
    can be consitently found for all subjects.
(4) Fixed: Output fpr batch for calculating TIV was not correct.
(5) Fixed: SPM alert windows blocked GUI in cat_stat_analyze_ROIs.m.
(6) Changed: In batch for estimating TIV at least one xml-file has to be
    selected.

------------------------------------------------------------------------
r1233 | gaser | 2017-12-04 00:26:25 +0100 (Mon, 04 Dec 2017) | 176 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_io_FreeSurfer.m
M       cat_run.m
M       cat_stat_TIV.m
M       cat_stat_analyze_ROIs.m
M       cat_stat_spm2x.m
M       cat_surf_info.m
M       cat_surf_parameters.m
M       cat_surf_resamp.m
M       cat_surf_results.m
M       cat_surf_smooth.m
M       cat_surf_surf2roi.m
M       cat_tst_qa_cleaner.m
M       cat_vol_slice_overlay_ui.m
A       check_pipeline
A       check_pipeline/IXI002-Guys-0828-T1.nii
A       check_pipeline/analysis
A       check_pipeline/analysis/surface
A       check_pipeline/analysis/surface/RPV.dat
A       check_pipeline/analysis/surface/RPV.gii
A       check_pipeline/analysis/surface/SPM.mat
A       check_pipeline/analysis/surface/spmF_0001.dat
A       check_pipeline/analysis/surface/spmF_0001.gii
A       check_pipeline/analysis/surface/spmT_0002.dat
A       check_pipeline/analysis/surface/spmT_0002.gii
A       check_pipeline/analysis/volume
A       check_pipeline/analysis/volume/RPV.nii
A       check_pipeline/analysis/volume/SPM.mat
A       check_pipeline/analysis/volume/spmF_0001.nii
A       check_pipeline/analysis/volume/spmT_0002.nii
A       check_pipeline/batch_surface_pipeline.m
A       check_pipeline/batch_volume_pipeline.m
A       check_pipeline/label
A       check_pipeline/label/catROI_IXI002-Guys-0828-T1.mat
A       check_pipeline/label/catROI_IXI002-Guys-0828-T1.xml
A       check_pipeline/label/catROI_IXI016-Guys-0697-T1.mat
A       check_pipeline/label/catROI_IXI016-Guys-0697-T1.xml
A       check_pipeline/label/catROI_IXI017-Guys-0698-T1.mat
A       check_pipeline/label/catROI_IXI017-Guys-0698-T1.xml
A       check_pipeline/label/catROI_IXI019-Guys-0702-T1.mat
A       check_pipeline/label/catROI_IXI019-Guys-0702-T1.xml
A       check_pipeline/label/catROI_IXI020-Guys-0700-T1.mat
A       check_pipeline/label/catROI_IXI020-Guys-0700-T1.xml
A       check_pipeline/label/catROI_IXI021-Guys-0703-T1.mat
A       check_pipeline/label/catROI_IXI021-Guys-0703-T1.xml
A       check_pipeline/label/catROI_IXI022-Guys-0701-T1.mat
A       check_pipeline/label/catROI_IXI022-Guys-0701-T1.xml
A       check_pipeline/label/catROI_IXI023-Guys-0699-T1.mat
A       check_pipeline/label/catROI_IXI023-Guys-0699-T1.xml
A       check_pipeline/label/catROI_IXI024-Guys-0705-T1.mat
A       check_pipeline/label/catROI_IXI024-Guys-0705-T1.xml
A       check_pipeline/label/catROI_IXI025-Guys-0852-T1.mat
A       check_pipeline/label/catROI_IXI025-Guys-0852-T1.xml
A       check_pipeline/label/catROI_IXI026-Guys-0696-T1.mat
A       check_pipeline/label/catROI_IXI026-Guys-0696-T1.xml
A       check_pipeline/label/catROI_IXI027-Guys-0710-T1.mat
A       check_pipeline/label/catROI_IXI027-Guys-0710-T1.xml
A       check_pipeline/label/catROI_IXI028-Guys-1038-T1.mat
A       check_pipeline/label/catROI_IXI028-Guys-1038-T1.xml
A       check_pipeline/label/catROI_IXI029-Guys-0829-T1.mat
A       check_pipeline/label/catROI_IXI029-Guys-0829-T1.xml
A       check_pipeline/label/catROI_IXI030-Guys-0708-T1.mat
A       check_pipeline/label/catROI_IXI030-Guys-0708-T1.xml
A       check_pipeline/label/catROI_IXI031-Guys-0797-T1.mat
A       check_pipeline/label/catROI_IXI031-Guys-0797-T1.xml
A       check_pipeline/label/catROI_IXI036-Guys-0736-T1.mat
A       check_pipeline/label/catROI_IXI036-Guys-0736-T1.xml
A       check_pipeline/label/catROI_IXI037-Guys-0704-T1.mat
A       check_pipeline/label/catROI_IXI037-Guys-0704-T1.xml
A       check_pipeline/label/catROI_IXI038-Guys-0729-T1.mat
A       check_pipeline/label/catROI_IXI038-Guys-0729-T1.xml
A       check_pipeline/label/catROI_IXI040-Guys-0724-T1.mat
A       check_pipeline/label/catROI_IXI040-Guys-0724-T1.xml
A       check_pipeline/label/catROIs_IXI002-Guys-0828-T1.mat
A       check_pipeline/label/catROIs_IXI002-Guys-0828-T1.xml
A       check_pipeline/label/catROIs_IXI016-Guys-0697-T1.mat
A       check_pipeline/label/catROIs_IXI016-Guys-0697-T1.xml
A       check_pipeline/label/catROIs_IXI017-Guys-0698-T1.mat
A       check_pipeline/label/catROIs_IXI017-Guys-0698-T1.xml
A       check_pipeline/label/catROIs_IXI019-Guys-0702-T1.mat
A       check_pipeline/label/catROIs_IXI019-Guys-0702-T1.xml
A       check_pipeline/label/catROIs_IXI020-Guys-0700-T1.mat
A       check_pipeline/label/catROIs_IXI020-Guys-0700-T1.xml
A       check_pipeline/label/catROIs_IXI021-Guys-0703-T1.mat
A       check_pipeline/label/catROIs_IXI021-Guys-0703-T1.xml
A       check_pipeline/label/catROIs_IXI022-Guys-0701-T1.mat
A       check_pipeline/label/catROIs_IXI022-Guys-0701-T1.xml
A       check_pipeline/label/catROIs_IXI023-Guys-0699-T1.mat
A       check_pipeline/label/catROIs_IXI023-Guys-0699-T1.xml
A       check_pipeline/label/catROIs_IXI024-Guys-0705-T1.mat
A       check_pipeline/label/catROIs_IXI024-Guys-0705-T1.xml
A       check_pipeline/label/catROIs_IXI025-Guys-0852-T1.mat
A       check_pipeline/label/catROIs_IXI025-Guys-0852-T1.xml
A       check_pipeline/label/catROIs_IXI026-Guys-0696-T1.mat
A       check_pipeline/label/catROIs_IXI026-Guys-0696-T1.xml
A       check_pipeline/label/catROIs_IXI027-Guys-0710-T1.mat
A       check_pipeline/label/catROIs_IXI027-Guys-0710-T1.xml
A       check_pipeline/label/catROIs_IXI028-Guys-1038-T1.mat
A       check_pipeline/label/catROIs_IXI028-Guys-1038-T1.xml
A       check_pipeline/label/catROIs_IXI029-Guys-0829-T1.mat
A       check_pipeline/label/catROIs_IXI029-Guys-0829-T1.xml
A       check_pipeline/label/catROIs_IXI030-Guys-0708-T1.mat
A       check_pipeline/label/catROIs_IXI030-Guys-0708-T1.xml
A       check_pipeline/label/catROIs_IXI031-Guys-0797-T1.mat
A       check_pipeline/label/catROIs_IXI031-Guys-0797-T1.xml
A       check_pipeline/label/catROIs_IXI036-Guys-0736-T1.mat
A       check_pipeline/label/catROIs_IXI036-Guys-0736-T1.xml
A       check_pipeline/label/catROIs_IXI037-Guys-0704-T1.mat
A       check_pipeline/label/catROIs_IXI037-Guys-0704-T1.xml
A       check_pipeline/label/catROIs_IXI038-Guys-0729-T1.mat
A       check_pipeline/label/catROIs_IXI038-Guys-0729-T1.xml
A       check_pipeline/label/catROIs_IXI040-Guys-0724-T1.mat
A       check_pipeline/label/catROIs_IXI040-Guys-0724-T1.xml
A       check_pipeline/mri
A       check_pipeline/mri/mwp1IXI002-Guys-0828-T1.nii
A       check_pipeline/mri/mwp1IXI016-Guys-0697-T1.nii
A       check_pipeline/mri/mwp1IXI017-Guys-0698-T1.nii
A       check_pipeline/mri/mwp1IXI019-Guys-0702-T1.nii
A       check_pipeline/report
A       check_pipeline/report/cat_IXI002-Guys-0828-T1.mat
A       check_pipeline/report/cat_IXI002-Guys-0828-T1.xml
A       check_pipeline/report/cat_IXI016-Guys-0697-T1.mat
A       check_pipeline/report/cat_IXI016-Guys-0697-T1.xml
A       check_pipeline/report/cat_IXI017-Guys-0698-T1.mat
A       check_pipeline/report/cat_IXI017-Guys-0698-T1.xml
A       check_pipeline/report/cat_IXI019-Guys-0702-T1.mat
A       check_pipeline/report/cat_IXI019-Guys-0702-T1.xml
A       check_pipeline/surf
A       check_pipeline/surf/lh.central.IXI002-Guys-0828-T1.gii
A       check_pipeline/surf/lh.central.IXI016-Guys-0697-T1.gii
A       check_pipeline/surf/lh.central.IXI017-Guys-0698-T1.gii
A       check_pipeline/surf/lh.central.IXI019-Guys-0702-T1.gii
A       check_pipeline/surf/lh.sphere.IXI002-Guys-0828-T1.gii
A       check_pipeline/surf/lh.sphere.IXI016-Guys-0697-T1.gii
A       check_pipeline/surf/lh.sphere.IXI017-Guys-0698-T1.gii
A       check_pipeline/surf/lh.sphere.IXI019-Guys-0702-T1.gii
A       check_pipeline/surf/lh.sphere.reg.IXI002-Guys-0828-T1.gii
A       check_pipeline/surf/lh.sphere.reg.IXI016-Guys-0697-T1.gii
A       check_pipeline/surf/lh.sphere.reg.IXI017-Guys-0698-T1.gii
A       check_pipeline/surf/lh.sphere.reg.IXI019-Guys-0702-T1.gii
A       check_pipeline/surf/lh.thickness.IXI002-Guys-0828-T1
A       check_pipeline/surf/lh.thickness.IXI016-Guys-0697-T1
A       check_pipeline/surf/lh.thickness.IXI017-Guys-0698-T1
A       check_pipeline/surf/lh.thickness.IXI019-Guys-0702-T1
A       check_pipeline/surf/rh.central.IXI002-Guys-0828-T1.gii
A       check_pipeline/surf/rh.central.IXI016-Guys-0697-T1.gii
A       check_pipeline/surf/rh.central.IXI017-Guys-0698-T1.gii
A       check_pipeline/surf/rh.central.IXI019-Guys-0702-T1.gii
A       check_pipeline/surf/rh.sphere.IXI002-Guys-0828-T1.gii
A       check_pipeline/surf/rh.sphere.IXI016-Guys-0697-T1.gii
A       check_pipeline/surf/rh.sphere.IXI017-Guys-0698-T1.gii
A       check_pipeline/surf/rh.sphere.IXI019-Guys-0702-T1.gii
A       check_pipeline/surf/rh.sphere.reg.IXI002-Guys-0828-T1.gii
A       check_pipeline/surf/rh.sphere.reg.IXI016-Guys-0697-T1.gii
A       check_pipeline/surf/rh.sphere.reg.IXI017-Guys-0698-T1.gii
A       check_pipeline/surf/rh.sphere.reg.IXI019-Guys-0702-T1.gii
A       check_pipeline/surf/rh.thickness.IXI002-Guys-0828-T1
A       check_pipeline/surf/rh.thickness.IXI016-Guys-0697-T1
A       check_pipeline/surf/rh.thickness.IXI017-Guys-0698-T1
A       check_pipeline/surf/rh.thickness.IXI019-Guys-0702-T1
M       html/cat_starting.html

(1) Added: check_pipeline to check volume as well as surface-based pipeline.
(2) Changed: Updated help text for quick start guide.
(3) Changed: cat_vol_slice_overlay now allows definition of xy-yorder and
    saved image.
(4) Fixed: Dependency output names for mayn functions.
(5) Fixed: Missing colorbar handle in cat_surf_results.m.
(6) Fixed: Some typos.


------------------------------------------------------------------------
r1232 | gaser | 2017-12-01 21:54:50 +0100 (Fri, 01 Dec 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.fig
M       html/cat.html

Fixed: cat12.fig was corrupt and parts of the GUI were not working.

------------------------------------------------------------------------
r1231 | gaser | 2017-12-01 00:14:37 +0100 (Fri, 01 Dec 2017) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_cat.m
M       cat_batch_cat.sh
M       cat_batch_long.sh
M       cat_batch_spm.sh
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
MM      cat_surf_coregvol2surf.m
M       cat_surf_results.m

(1) Fixed: Filename for saving png-files in cat_surf_results was mixed up.
(2) Changed: Added print option to cat_defaults.m to suppress graphical
    output on clusters.
(3) Changed: Added "-jvm" flag to shell scripts that call matlab.

------------------------------------------------------------------------
r1230 | gaser | 2017-11-30 09:24:15 +0100 (Thu, 30 Nov 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m
M       cat_surf_info.m

Fixed: Handling with multiple 32k meshes in cat_surf_info.m


------------------------------------------------------------------------
r1229 | gaser | 2017-11-29 22:03:22 +0100 (Wed, 29 Nov 2017) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat12.fig
M       cat12.m
M       cat_conf_stools.m
A       cat_surf_coregvol2surf.m
M       cat_vol_nonlin_coreg_multi_run.m

(1) Changed: Added new batch for combining non-linear co-registration and
    mapping of (co-registered) volumes to surface in native space.
(2) Changed: Removed experimental code for combining non-linear co-registration
    and volume mapping that did not worked.

------------------------------------------------------------------------
r1228 | gaser | 2017-11-29 19:21:06 +0100 (Wed, 29 Nov 2017) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m
M       cat_surf_info.m
M       cat_surf_vol2surf.m

(1) Fixed: Nearest Neighbour interpolation for isocolors2.m was not correct.
(2) Changed: Added functionality for 4d files for cat_surf_vol2surf.m
(3) Fixed: Handling of 32k meshes in cat_surf_info.m

------------------------------------------------------------------------
r1227 | gaser | 2017-11-29 09:20:32 +0100 (Wed, 29 Nov 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_showslice_all.m
M       cat_surf_results.m

(1) Fixed: First filename for cat_stat_showslice_all.m was not printed.
(2) Changed: Location for GUI elements in cat_surf_results are now more
    broader.

------------------------------------------------------------------------
r1226 | gaser | 2017-11-28 15:25:06 +0100 (Tue, 28 Nov 2017) | 27 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_amap.mexw64
M       cat_ornlm.mexw64
M       cat_sanlm.mexw64
M       cat_vbdist.mexw64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexw64
M       cat_vol_pbtp.mexw64
M       cat_vol_simgrow.mexw64
 M      development/Template_4_IXI555_MNI152_GS1mm_corr.nii
M       html/cat.html
 M      templates_surfaces_32k/lh.patch.freesurfer.gii
 M      templates_surfaces_32k/rh.patch.freesurfer.gii
 M      templates_surfaces_32k/templates_surfaces_32k.man

Changed: Recompiled mex-files with Matlab 2017b under Windows.

------------------------------------------------------------------------
r1225 | gaser | 2017-11-21 13:05:25 +0100 (Tue, 21 Nov 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m

Changed: Added printout of selected filename in cat_surf_resulrs.m

------------------------------------------------------------------------
r1224 | gaser | 2017-11-21 12:03:41 +0100 (Tue, 21 Nov 2017) | 29 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       atlases_surfaces_32k/lh.aparc_DK40.freesurfer.annot
D       atlases_surfaces_32k/lh.aparc_DKT40JT.freesurfer.annot
M       atlases_surfaces_32k/lh.aparc_HCP_MMP1.freesurfer.annot
M       atlases_surfaces_32k/lh.aparc_a2009s.freesurfer.annot
M       atlases_surfaces_32k/rh.aparc_DK40.freesurfer.annot
D       atlases_surfaces_32k/rh.aparc_DKT40JT.freesurfer.annot
M       atlases_surfaces_32k/rh.aparc_HCP_MMP1.freesurfer.annot
M       atlases_surfaces_32k/rh.aparc_a2009s.freesurfer.annot
A       development/Template_4_IXI555_MNI152_GS1mm_corr.nii
M       html/cat.html
M       templates_surfaces/lh.mask
M       templates_surfaces/rh.mask
M       templates_surfaces/templates_surfaces.man
M       templates_surfaces_32k/lh.central.Template_T1_IXI555_MNI152_GS.gii
M       templates_surfaces_32k/lh.inflated.freesurfer.gii
M       templates_surfaces_32k/lh.mask
M       templates_surfaces_32k/lh.sphere.freesurfer.gii
M       templates_surfaces_32k/rh.central.Template_T1_IXI555_MNI152_GS.gii
M       templates_surfaces_32k/rh.inflated.freesurfer.gii
M       templates_surfaces_32k/rh.mask
M       templates_surfaces_32k/rh.sphere.freesurfer.gii
M       templates_surfaces_32k/templates_surfaces_32k.man

(1) Changed: Updated description of surface templates.
(2) Changed: Updated 32k HCP meshes w.r.t. new sphere surfaces.

------------------------------------------------------------------------
r1223 | gaser | 2017-11-20 22:39:49 +0100 (Mon, 20 Nov 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_results.m
M       html/cat.html

Fixed: Path is now also used while saving png file in cat_surf_results.m

------------------------------------------------------------------------
r1222 | gaser | 2017-11-20 17:17:23 +0100 (Mon, 20 Nov 2017) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_display.m
M       cat_surf_results.m
M       html/cat.html
A       templates_surfaces_32k/lh.patch.freesurfer.gii
A       templates_surfaces_32k/rh.patch.freesurfer.gii
A       templates_surfaces_32k/templates_surfaces_32k.man

(1) Added: Flat maps and desriptions added for 32k HCP meshes.
(2) Fixed: Corrected views for flat maps.
(3) Fixed: Coorected typo in cat_surf_display.m from last changes.

------------------------------------------------------------------------
r1221 | gaser | 2017-11-20 14:47:20 +0100 (Mon, 20 Nov 2017) | 38 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
 M      atlases_surfaces_32k/lh.aparc_DK40.freesurfer.annot
 M      atlases_surfaces_32k/lh.aparc_DKT40JT.freesurfer.annot
 M      atlases_surfaces_32k/lh.aparc_HCP_MMP1.freesurfer.annot
 M      atlases_surfaces_32k/lh.aparc_a2009s.freesurfer.annot
 M      atlases_surfaces_32k/rh.aparc_DK40.freesurfer.annot
 M      atlases_surfaces_32k/rh.aparc_DKT40JT.freesurfer.annot
 M      atlases_surfaces_32k/rh.aparc_HCP_MMP1.freesurfer.annot
 M      atlases_surfaces_32k/rh.aparc_a2009s.freesurfer.annot
M       cat_surf_render2.m
M       html/cat.html
 M      templates_surfaces/lh.mc.freesurfer.gii
 M      templates_surfaces/lh.sqrtsulc.freesurfer.gii
 M      templates_surfaces/rh.mc.freesurfer.gii
 M      templates_surfaces/rh.sqrtsulc.freesurfer.gii
 M      templates_surfaces_32k/fsavg.index2D_256x128.txt
 M      templates_surfaces_32k/lh.central.Template_T1_IXI555_MNI152_GS.gii
 M      templates_surfaces_32k/lh.central.freesurfer.gii
 M      templates_surfaces_32k/lh.inflated.freesurfer.gii
 M      templates_surfaces_32k/lh.mask
 M      templates_surfaces_32k/lh.mc.freesurfer.gii
 M      templates_surfaces_32k/lh.sphere.freesurfer.gii
 M      templates_surfaces_32k/lh.sqrtsulc.freesurfer.gii
 M      templates_surfaces_32k/mesh.central.freesurfer.gii
 M      templates_surfaces_32k/rh.central.Template_T1_IXI555_MNI152_GS.gii
 M      templates_surfaces_32k/rh.central.freesurfer.gii
 M      templates_surfaces_32k/rh.inflated.freesurfer.gii
 M      templates_surfaces_32k/rh.mask
 M      templates_surfaces_32k/rh.mc.freesurfer.gii
 M      templates_surfaces_32k/rh.sphere.freesurfer.gii
 M      templates_surfaces_32k/rh.sqrtsulc.freesurfer.gii

Changed: Made code compatible with filenames with _32k that indicate lower
resoluted 32k meshes.


------------------------------------------------------------------------
r1220 | gaser | 2017-11-20 14:34:33 +0100 (Mon, 20 Nov 2017) | 18 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_nonlin_coreg.m
M       cat_conf_stools.m
M       cat_surf_display.m
M       cat_surf_info.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
M       cat_vol_nonlin_coreg.m
M       cat_vol_nonlin_coreg_multi_run.m
M       html/cat.html

(1) Changed: Made code compatible with filenames with _32k that indicate
    lower resoluted 32k meshes.
(2) Changed: Added bounding box option to non-linear co-registration.
(3) Changed: Recompiled CAT-code.

------------------------------------------------------------------------
r1219 | gaser | 2017-11-20 00:28:59 +0100 (Mon, 20 Nov 2017) | 63 lines

Changed paths:
M       CHANGES.txt
M       Makefile
A       atlases_surfaces_32k
A       atlases_surfaces_32k/lh.aparc_DK40.freesurfer.annot
A       atlases_surfaces_32k/lh.aparc_DKT40JT.freesurfer.annot
A       atlases_surfaces_32k/lh.aparc_HCP_MMP1.freesurfer.annot
A       atlases_surfaces_32k/lh.aparc_a2009s.freesurfer.annot
A       atlases_surfaces_32k/rh.aparc_DK40.freesurfer.annot
A       atlases_surfaces_32k/rh.aparc_DKT40JT.freesurfer.annot
A       atlases_surfaces_32k/rh.aparc_HCP_MMP1.freesurfer.annot
A       atlases_surfaces_32k/rh.aparc_a2009s.freesurfer.annot
M       cat12.m
M       cat_conf_stools.m
M       cat_stat_check_cov.m
M       cat_stat_cva_ui.m
M       cat_stat_spm2x.m
M       cat_surf_calc.m
M       cat_surf_createCS.m
M       cat_surf_display.m
M       cat_surf_fun.m
M       cat_surf_info.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
M       cat_surf_results.m
M       cat_update.m
D       templates_surfaces/lh.mc.central.freesurfer.gii
A       templates_surfaces/lh.mc.freesurfer.gii
D       templates_surfaces/lh.sqrtsulc.central.freesurfer.gii
A       templates_surfaces/lh.sqrtsulc.freesurfer.gii
D       templates_surfaces/rh.mc.central.freesurfer.gii
A       templates_surfaces/rh.mc.freesurfer.gii
D       templates_surfaces/rh.sqrtsulc.central.freesurfer.gii
A       templates_surfaces/rh.sqrtsulc.freesurfer.gii
M       templates_surfaces/templates_surfaces.man
A       templates_surfaces_32k
A       templates_surfaces_32k/fsavg.index2D_256x128.txt
A       templates_surfaces_32k/lh.central.Template_T1_IXI555_MNI152_GS.gii
A       templates_surfaces_32k/lh.central.freesurfer.gii
A       templates_surfaces_32k/lh.inflated.freesurfer.gii
A       templates_surfaces_32k/lh.mask
A       templates_surfaces_32k/lh.mc.freesurfer.gii
A       templates_surfaces_32k/lh.sphere.freesurfer.gii
A       templates_surfaces_32k/lh.sqrtsulc.freesurfer.gii
A       templates_surfaces_32k/mesh.central.freesurfer.gii
A       templates_surfaces_32k/rh.central.Template_T1_IXI555_MNI152_GS.gii
A       templates_surfaces_32k/rh.central.freesurfer.gii
A       templates_surfaces_32k/rh.inflated.freesurfer.gii
A       templates_surfaces_32k/rh.mask
A       templates_surfaces_32k/rh.mc.freesurfer.gii
A       templates_surfaces_32k/rh.sphere.freesurfer.gii
A       templates_surfaces_32k/rh.sqrtsulc.freesurfer.gii

(1) Changed: Added remsampling to 32k mesh from Human Connectome Project
    (HCP). This allows faster and less memory demanding processing and
    provides compatibility to the HCP. Another advantage is that left and
    right hemispheres are aligned to optionally allow a direct comparison
    between hemispheres.
(2) Changed: Made all necessary functions compatible to 32k meshes.
(3) Added: New folders templates_surfaces_32k and atlases_surfaces_32k
(4) Fixed: Camlight and axes issue in cat_surf_results.m
(5) Changed: Renamed some files in templates_surfaces.

------------------------------------------------------------------------
r1218 | dahnke | 2017-11-17 17:27:43 +0100 (Fri, 17 Nov 2017) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_cleanup.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_surf_createCS.m
M       cat_vol_pbt.m
M       html/images/cat_tst_seg_bwp_ana.png

Update:  Renamed command-lined output cmdln_*.txt into catlog_*.txt.


------------------------------------------------------------------------
r1217 | dahnke | 2017-11-16 18:13:37 +0100 (Thu, 16 Nov 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_run_job.m

Update:  Add command-line output to XML report structure.


------------------------------------------------------------------------
r1216 | dahnke | 2017-11-16 16:58:12 +0100 (Thu, 16 Nov 2017) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_io_report.m
M       cat_main.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_surf_createCS.m
M       html/images/cat_tst_seg_bwp_ana.png

New:    Added command line output for the main preprocessing of one subject that
        writes a text file "cmdln_*.txt" into the report directory.
Fixed:  Corrected output format of processing time in the command line.


------------------------------------------------------------------------
r1215 | dahnke | 2017-11-15 15:31:29 +0100 (Wed, 15 Nov 2017) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_main_registration.m
M       cat_run_job.m
M       cat_run_job1070.m
M       tbx_cfg_cat.m

Deleted: Removed check of the relative volume of the initial SPM preprocessing
         in "cat_run" and "cat_run_job1070" because the use parameter did not
         describe the volume.

------------------------------------------------------------------------
r1214 | dahnke | 2017-11-13 12:08:55 +0100 (Mon, 13 Nov 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_run.m
M       html/images/cat_tst_seg_bwp_ana.png

Fixed:    Corrected error data structure error of the atlas definition of the
          cat.extopts and cat.output variable.

------------------------------------------------------------------------
r1213 | gaser | 2017-11-10 16:10:52 +0100 (Fri, 10 Nov 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_main_registration.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_createCS.m

(1) Fixed: Removed debugging code that caused crash.
(2) Changed: Added faster option for CAT_Surf2Sphere in cat_surf_createCS.m

------------------------------------------------------------------------
r1212 | dahnke | 2017-11-10 13:39:37 +0100 (Fri, 10 Nov 2017) | 45 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_io_FreeSurfer.m
M       cat_io_cmd.m
M       cat_io_xml.m
M       cat_main.m
M       cat_main_registration.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_run_job_APP_SPM.m
M       cat_surf_avg.m
M       cat_surf_createCS.m
M       cat_surf_render2.m
M       cat_vol_resize.m
M       cat_vol_sanlm.m
M       cat_vol_smooth3X.m
M       cat_vol_urqio.m
M       html/images/cat_tst_reg_boxplot.png
M       html/images/cat_tst_seg_bwp_ana.png
M       internal/cat_vol_nlmus.m
M       tbx_cfg_cat.m

(1)  Fixed:   Write MAT file before XML file in cat_io_xml to catch XML writing
              errors, e.g. on server.
(2)  Fixed:   Move "printCATreport" settings behind QA and XML report output.
(3)  Fixed:   Corrections in internal NLM-interpolation "cat_vol_nlmus".
(4)  Fixed:   Updated NLM filter options, resolution options, and intensity
              limits in cat_run_job1070 based on changes of in cat_run_job.
(5)  Update:  Changed of ultra high resolution scripts (cat_conf_tools and
              cat_vol_urqio.
(6)  Fixed:   Small corrections/modifications in cat_io_cmd.
(7)  Fixed:   Surface processing do not require Shooting/Dartel registration
              Developer options for fast surface processing in cat_surf_createCS.
(8)  Fixed:   Corrections (rigid vs. affine shooting) and cleanup in
              cat_main_registration.
(9)  Fixed:   Error with lazy processing developer option (cat_run).
(10) Update:  Less options for APP1 and APP2 processing.
(11) New:     Estimation of the standard deviation in cat_vol_resize.
(12) Fixed:   Added histogram scaling in cat_vol_sanlm to avoid problems with
              untypical scaled data.
(13) Fixed:   Small error in cat_vol_smooth3X.
(14) Fixed:   Typos in CHANGES.txt.

------------------------------------------------------------------------
r1211 | gaser | 2017-11-09 15:43:30 +0100 (Thu, 09 Nov 2017) | 23 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_run.m
 M      development/Template_0_IXI555_MNI152_GS1mm.nii
 M      development/Template_1_IXI555_MNI152_GS1mm.nii
 M      development/Template_2_IXI555_MNI152_GS1mm.nii
 M      development/Template_3_IXI555_MNI152_GS1mm.nii
 M      development/Template_4_IXI555_MNI152_GS1mm.nii
M       html/cat.html
 M      templates_1.50mm/Template_T1_IXI555_MNI152_GS.nii
 M      templates_surfaces/lc.central.Template_T1_IXI555_MNI152_GS.gii
 M      templates_surfaces/lc.thickness.Template_T1_IXI555_MNI152_GS
 M      templates_surfaces/lh.central.Template_T1_IXI555_MNI152_GS.gii
 M      templates_surfaces/lh.thickness.Template_T1_IXI555_MNI152_GS
 M      templates_surfaces/rc.central.Template_T1_IXI555_MNI152_GS.gii
 M      templates_surfaces/rc.thickness.Template_T1_IXI555_MNI152_GS
 M      templates_surfaces/rh.central.Template_T1_IXI555_MNI152_GS.gii
 M      templates_surfaces/rh.thickness.Template_T1_IXI555_MNI152_GS

Fixed: Customized templates start with *Template_0* which was not considered
in cat_run.m

------------------------------------------------------------------------
r1210 | gaser | 2017-11-08 16:08:14 +0100 (Wed, 08 Nov 2017) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
MM      cat_surf_max.m
M       cat_surf_vol2surf.m
M       html/cat.html

(1) Fixed: Mapping of volumes to surfaces is now correctly working. The
    starting point is now always according to the central surface and positive
    values point inwards (to the WM boundary) and negative values outwards
    to the pial surface.
(2) Changed: Changed start and end values for volume mapping.
(3) Changed: recompiled CAT code.


------------------------------------------------------------------------
r1209 | gaser | 2017-11-07 17:20:27 +0100 (Tue, 07 Nov 2017) | 49 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Contents_info.txt
M       batches/cattest/cat12_201_VBM_deformation.m
M       batches/cattest/cat12_302_SBM_MapNormVol2AvgSurf.m
M       cat_conf_stools.m
M       cat_roi_roi2surf.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_display.m
M       cat_surf_render2.m
M       cat_surf_results.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_rgb_ui.m
M       cat_vol_slice_overlay_ui.m
A       development/Template_0_IXI555_MNI152_GS1mm.nii
A       development/Template_1_IXI555_MNI152_GS1mm.nii
A       development/Template_2_IXI555_MNI152_GS1mm.nii
A       development/Template_3_IXI555_MNI152_GS1mm.nii
A       development/Template_4_IXI555_MNI152_GS1mm.nii
M       html/cat.html
M       html/cat.txt
D       templates_1.50mm/Template_T1_IXI555_MNI152.nii
A       templates_1.50mm/Template_T1_IXI555_MNI152_GS.nii
D       templates_surfaces/lc.central.Template_T1_IXI555_MNI152.gii
A       templates_surfaces/lc.central.Template_T1_IXI555_MNI152_GS.gii
D       templates_surfaces/lc.thickness.Template_T1_IXI555_MNI152
A       templates_surfaces/lc.thickness.Template_T1_IXI555_MNI152_GS
D       templates_surfaces/lh.central.Template_T1_IXI555_MNI152.gii
A       templates_surfaces/lh.central.Template_T1_IXI555_MNI152_GS.gii
D       templates_surfaces/lh.thickness.Template_T1_IXI555_MNI152
A       templates_surfaces/lh.thickness.Template_T1_IXI555_MNI152_GS
D       templates_surfaces/rc.central.Template_T1_IXI555_MNI152.gii
A       templates_surfaces/rc.central.Template_T1_IXI555_MNI152_GS.gii
D       templates_surfaces/rc.thickness.Template_T1_IXI555_MNI152
A       templates_surfaces/rc.thickness.Template_T1_IXI555_MNI152_GS
D       templates_surfaces/rh.central.Template_T1_IXI555_MNI152.gii
A       templates_surfaces/rh.central.Template_T1_IXI555_MNI152_GS.gii
D       templates_surfaces/rh.thickness.Template_T1_IXI555_MNI152
A       templates_surfaces/rh.thickness.Template_T1_IXI555_MNI152_GS
M       templates_surfaces/templates_surfaces.man

(1) Changed: Replaced average T1 Template_T1_IXI555_MNI152.nii by a more detailed
    average of normalized images using Geodesic Shooting (GS).
(2) Changed: Replaced template surfaces of Template_T1_IXI555_MNI152.nii by a more
    detailed surface of normalized images using Geodesic Shooting (GS).
(3) Changed: Recompiled CAT-code.


------------------------------------------------------------------------
r1208 | gaser | 2017-11-06 17:08:35 +0100 (Mon, 06 Nov 2017) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_spm2x.m
A       cat_surf_max.m
M       cat_surf_results.m
M       html/cat.html

(1) Added: cat_surf_max.m as modified version of spm_mesh_max because for some
    rare data only one global maximum was returned.
(2) Changed: Replaced spm_mesh_max by cat_surf_max in cat_stat_spm2x.m.

------------------------------------------------------------------------
r1207 | gaser | 2017-10-27 10:00:34 +0200 (Fri, 27 Oct 2017) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.fig
M       cat_surf_display.m
M       html/cat.html

(1) Fixed: cat_surf_display now correctly works with merged meshes.
(2) Changed: Size and proportions of cat12 windows are now better balanced
    between different matlab versions and screen sizes.

------------------------------------------------------------------------
r1206 | gaser | 2017-10-25 10:19:06 +0200 (Wed, 25 Oct 2017) | 10 lines

Changed paths:
M       CHANGES.txt
MM      cat_conf_nonlin_coreg.m
M       cat_conf_stools.m
MM      cat_vol_nonlin_coreg.m
MM      cat_vol_nonlin_coreg_multi_run.m

Changed: Limited batch for non-linear co-registration to one subject
which eases the combination with surface mapping and other batches.

------------------------------------------------------------------------
r1205 | gaser | 2017-10-24 23:02:09 +0200 (Tue, 24 Oct 2017) | 8 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt

Changed: Updated CAT12 manual regarding the forced use of "overall mean"
for centering covariates.

------------------------------------------------------------------------
r1204 | gaser | 2017-10-24 16:54:48 +0200 (Tue, 24 Oct 2017) | 17 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.fig
A       cat_conf_nonlin_coreg.m
M       cat_conf_tools.m
M       cat_long_multi_run.m
M       cat_surf_results.m
A       cat_vol_nonlin_coreg.m
A       cat_vol_nonlin_coreg_multi_run.m
M       html/cat.html
M       html/cat.txt

(1) Added: Added batch for non-linear co-registration.
(2) Fixed: Camlight and scaling issue with flatmaps in cat_surf_results.m
(3) Fixed: Batchmode dependencies for longit. pipeline

------------------------------------------------------------------------
r1203 | gaser | 2017-10-23 17:47:38 +0200 (Mon, 23 Oct 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_results.m
MM      cat_vol_slice_overlay_rgb_ui.m
M       html/cat.html

Fixed: File selection error in cat_surf_results.m

------------------------------------------------------------------------
r1202 | gaser | 2017-10-23 13:15:20 +0200 (Mon, 23 Oct 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_surf_results.m

Fixed: Removed some smaller bugs for multiple results view in cat_surf_results.m

------------------------------------------------------------------------
r1201 | gaser | 2017-10-20 09:29:13 +0200 (Fri, 20 Oct 2017) | 12 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
A       cat_vol_slice_overlay_rgb_ui.m
M       html/cat.html
M       html/cat_starting.html

Added: Added example to use RGB overlay of up to 3 files with slice_overlay.


------------------------------------------------------------------------
r1200 | gaser | 2017-10-19 00:24:24 +0200 (Thu, 19 Oct 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m
 M      templates_surfaces/mesh.central.freesurfer.gii

Changed: Updated cat_surf_results to now deal with multiple results that
can be slected using ui.

------------------------------------------------------------------------
r1199 | gaser | 2017-10-19 00:22:40 +0200 (Thu, 19 Oct 2017) | 8 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
!       cat_surf_results.m

Changed: Updated manual w.r.t. re-use of customized DARTEL templates.

------------------------------------------------------------------------
r1198 | gaser | 2017-10-17 14:55:29 +0200 (Tue, 17 Oct 2017) | 17 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat12.m
M       cat_surf_info.m
M       cat_surf_results.m
M       html/cat_methods_RBM.html
M       html/cat_starting.html
A       templates_surfaces/mesh.central.freesurfer.gii
M       templates_surfaces/templates_surfaces.man

(1) Changed: Finished preparing all tools for dealing with merged left and
    right hemipsheres. Cerebellar merging is not yet fully supported.
(2) Changed: Updated online help and CAT12 manual w.r.t. merged meshes.
(3) Added: Added merged mesh for fsaverage central surface.

------------------------------------------------------------------------
r1197 | gaser | 2017-10-17 09:20:31 +0200 (Tue, 17 Oct 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_display.m

Changed: Check whether rng function exists in cat_surf_display.m

------------------------------------------------------------------------
r1196 | gaser | 2017-10-17 08:30:51 +0200 (Tue, 17 Oct 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_display.m
M       cat_surf_info.m

Changed: Prepared display function for dealing with merged hemisphere meshes.

------------------------------------------------------------------------
r1195 | gaser | 2017-10-17 00:31:44 +0200 (Tue, 17 Oct 2017) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_conf_stools.m
M       cat_stat_check_cov.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
 M      templates_surfaces/lh.patch.freesurfer.gii
 M      templates_surfaces/lh.sqrtsulc.central.freesurfer.gii
 M      templates_surfaces/rh.patch.freesurfer.gii
 M      templates_surfaces/rh.sqrtsulc.central.freesurfer.gii

Changed: Prepared some function for dealing with merged hemisphere meshes.

------------------------------------------------------------------------
r1194 | gaser | 2017-10-11 17:06:05 +0200 (Wed, 11 Oct 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_surf_results.m

Changed: Added mapping function to use weighted average with gaussian kernel
so that values at the border are weighted with 50% and center with 100% with
a gaussian shape.

------------------------------------------------------------------------
r1193 | gaser | 2017-10-11 00:45:20 +0200 (Wed, 11 Oct 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m
M       templates_surfaces/templates_surfaces.man

(1) Changed: Added flatmap view and atlas border overlay to
    cat_surf_results.m
(2) Changed: Upadted surface template description.

------------------------------------------------------------------------
r1192 | gaser | 2017-10-09 17:54:51 +0200 (Mon, 09 Oct 2017) | 17 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_render.m
M       cat_surf_render2.m
M       cat_surf_results.m
M       html/cat.html
A       templates_surfaces/lh.patch.freesurfer.gii
A       templates_surfaces/lh.sqrtsulc.central.freesurfer.gii
A       templates_surfaces/rh.patch.freesurfer.gii
A       templates_surfaces/rh.sqrtsulc.central.freesurfer.gii
M       templates_surfaces/templates_surfaces.man

(1) Changed: Added option to change underlying texture in cat_surf_results.m
(2) Fixed: Some small fixes for displaying annotations in cat_surf_render*.m
(3) Added: Added surface patches and silcal depth maps for fsaverage.

------------------------------------------------------------------------
r1191 | gaser | 2017-10-09 00:08:12 +0200 (Mon, 09 Oct 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m

Changed: Force to use OpenGL renderer in cat_surf_results.m

------------------------------------------------------------------------
r1190 | gaser | 2017-09-26 11:19:08 +0200 (Tue, 26 Sep 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m

Fixed: Function to hide neg. values in cat_surf_results.m was using wrong
parameters.

------------------------------------------------------------------------
r1189 | gaser | 2017-09-26 11:01:53 +0200 (Tue, 26 Sep 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m

Fixed: Function to hide neg. values in cat_surf_results.m was using wrong
parameters.

------------------------------------------------------------------------
r1188 | gaser | 2017-09-24 16:41:12 +0200 (Sun, 24 Sep 2017) | 8 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt

Changed: Updated CAT12 manual.


------------------------------------------------------------------------
r1187 | gaser | 2017-09-15 16:06:21 +0200 (Fri, 15 Sep 2017) | 9 lines

Changed paths:
M       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_stat_polynomial.m
M       html/cat_starting.html

Changed: Updated CAT12 manual and some help text.

------------------------------------------------------------------------
r1186 | gaser | 2017-09-14 16:58:48 +0200 (Thu, 14 Sep 2017) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_cat.m
M       cat_batch_long.m
M       cat_defaults.m
M       cat_system.m
M       html/cat.html

(1) Fixed: Batch mode is now correctly using defined default files.
(2) Changed: Updated comments in cat_defaults.m

------------------------------------------------------------------------
r1185 | gaser | 2017-09-13 17:02:47 +0200 (Wed, 13 Sep 2017) | 20 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_io_FreeSurfer.m
M       cat_surf_results.m
M       cat_vol_ROIval.c
M       cat_vol_downcut.c
M       cat_vol_eidist.c
M       cat_vol_eikonal3.c
M       cat_vol_genus0.c
M       cat_vol_gradient3.c
M       cat_vol_localstat.c
M       cat_vol_median3.c
M       cat_vol_simgrow.c
M       html/cat.html

(1) Changed: Updated interanl function names where vbm_ was still used.
(2) Fixed: Added warning if no hemipshere information could be found for
    cat_surf_results.m

------------------------------------------------------------------------
r1184 | dahnke | 2017-09-08 19:02:40 +0200 (Fri, 08 Sep 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_run_job_APP_final.m

(1) Fixed:  Corrected bug in cat_run_job1070.

------------------------------------------------------------------------
r1183 | dahnke | 2017-09-08 18:45:08 +0200 (Fri, 08 Sep 2017) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_main.m
M       cat_main_registration.m
M       cat_run_job_APP_final.m
M       cat_surf_avg.m
M       cat_surf_createCS.m
M       cat_surf_render2.m
M       cat_version.m
M       cat_vol_isarnlm.m
M       tbx_cfg_cat.m

(1) Changed:   Added option to use WM width/depth/thickness estimation.
(2) Fixed:     Updated do_dartel variable.
(3) Fixed:     Version estimation error due to flipped order in CHANGES.txt

------------------------------------------------------------------------
r1182 | gaser | 2017-09-08 16:00:55 +0200 (Fri, 08 Sep 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       svn_ci_log

Changed: Updated svn log system

------------------------------------------------------------------------
r1181 | gaser | 2017-09-08 15:58:41 +0200 (Fri, 08 Sep 2017) | 7 lines

Changed paths:
 M      CAT12-Manual.docx
M       CHANGES.txt
M       svn_ci_log

Changed: Updated svn log system

------------------------------------------------------------------------
r1180 | gaser | 2017-09-08 15:57:53 +0200 (Fri, 08 Sep 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       html/cat.html
M       svn_ci_log

Changed: Updated svn log system

------------------------------------------------------------------------
r1179 | gaser | 2017-09-08 15:53:42 +0200 (Fri, 08 Sep 2017) | 16 lines

Changed paths:
D       CAT12-Manual.doc
A       CAT12-Manual.docx
M       CAT12-Manual.pdf
M       CHANGES.txt
M       svn_ci_log
M       templates_surfaces/lc.central.freesurfer.gii
M       templates_surfaces/lc.sphere.freesurfer.gii
M       templates_surfaces/rc.central.freesurfer.gii
M       templates_surfaces/rc.sphere.freesurfer.gii
M       templates_surfaces/templates_surfaces.man

(1) Changed: Updated cerebellar templates
(2) Changed: Updated help text for surface templates
(3) Changed: Updated CAT12 manual

------------------------------------------------------------------------
r1178 | gaser | 2017-09-08 12:48:13 +0200 (Fri, 08 Sep 2017) | 34 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.fig
M       cat12.m
M       cat_amap.mexw64
M       cat_ornlm.mexw64
M       cat_run_job1070.m
M       cat_sanlm.mexw64
M       cat_surf_createCS.m
M       cat_vbdist.mexw64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexw64
M       cat_vol_pbtp.mexw64
M       cat_vol_simgrow.mexw64
M       html/cat.html
M       tbx_cfg_cat.m
M       templates_1.50mm/anatomy.txt
M       templates_1.50mm/cobra.txt

(1) Changed: For cerebellar hemisphere processing voxel size is now considered
    for reducing patches and refinement and interanl resolution.
(2) Changed: Updated some help text.
(3) Changed: Added and updated help text for atlases.


------------------------------------------------------------------------
r1177 | gaser | 2017-09-07 15:30:49 +0200 (Thu, 07 Sep 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat12.fig
M       cat12.m

Fixed: Corrected font size and CAT12 windows size for windows.

------------------------------------------------------------------------
r1176 | gaser | 2017-09-07 15:00:45 +0200 (Thu, 07 Sep 2017) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_io_report.m
M       cat_run_newcatch.m
M       cat_surf_createCS.m
M       compile.m
M       html/cat.html

(1) Fixed: Updated error output that was not correctly working for windows.
(2) Changed: Added warning for compiling under Mac with Matlab version < 9.2.
(3) Changed: Easier check for cerebellar preprocessing in cat_surf_createCS.m

------------------------------------------------------------------------
r1175 | dahnke | 2017-09-06 16:45:25 +0200 (Wed, 06 Sep 2017) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_io_writenii.m
M       cat_io_xml.m
M       cat_run.m
M       tbx_cfg_cat.m

(1) Changed:   Updated ROI GUI option in tbx_cfg_cat and job interpretation in
               cat_run_job.
(2) Changed:   Updated ROI structure in cat_defaults (same behaviour as before).
(3) Fixed:     Do not write XMLs in case of no JVM or in deployed mode.



------------------------------------------------------------------------
r1174 | gaser | 2017-09-05 19:26:10 +0200 (Tue, 05 Sep 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_io_report.m
M       spm_cat12.m

Changed: Updated warning when CAT binries are not working.

------------------------------------------------------------------------
r1173 | gaser | 2017-08-31 16:12:04 +0200 (Thu, 31 Aug 2017) | 21 lines

Changed paths:
M       CHANGES.txt
M       cat_amap.mexw64
M       cat_ornlm.mexw64
M       cat_sanlm.mexw64
M       cat_vbdist.mexw64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexw64
M       cat_vol_pbtp.mexw64
M       cat_vol_simgrow.mexw64

Fixed: Updated and recompiled some c-files.

------------------------------------------------------------------------
r1172 | gaser | 2017-08-31 15:19:22 +0200 (Thu, 31 Aug 2017) | 57 lines

Changed paths:
M       CHANGES.txt
M       cat_amap.c
M       cat_amap.mexa64
M       cat_amap.mexmaci64
M       cat_amap.mexw64
M       cat_ornlm.c
M       cat_ornlm.mexa64
M       cat_ornlm.mexmaci64
M       cat_ornlm.mexw64
M       cat_sanlm.c
M       cat_sanlm.mexa64
M       cat_sanlm.mexmaci64
M       cat_sanlm.mexw64
M       cat_vbdist.c
M       cat_vbdist.mexmaci64
M       cat_vbdist.mexw64
M       cat_vol_downcut.c
M       cat_vol_downcut.mexmaci64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.c
M       cat_vol_eidist.mexmaci64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.c
M       cat_vol_genus0.mexa64
M       cat_vol_genus0.mexmaci64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mexmaci64
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mexmaci64
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.c
M       cat_vol_laplace3.mexmaci64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.c
M       cat_vol_laplace3R.mexmaci64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexmaci64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexmaci64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexmaci64
M       cat_vol_median3c.mexw64
M       cat_vol_pbtp.cpp
M       cat_vol_pbtp.mexmaci64
M       cat_vol_pbtp.mexw64
M       cat_vol_simgrow.c
M       cat_vol_simgrow.mexmaci64
M       cat_vol_simgrow.mexw64
MM      cat_vol_urqio.m
M       compile.m
M       genus0.c
M       internal/cat_vol_cMRegularizarNLM3D.c
M       internal/cat_vol_cMRegularizarNLM3D.mexmaci64

Fixed: Updated and recompiled c-files that now also support Matlab R2017a for OSX.

------------------------------------------------------------------------
r1171 | gaser | 2017-08-31 10:41:59 +0200 (Thu, 31 Aug 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_surf_createCS.m
M       cat_tst_CJV.m

Fixed: Typos...

------------------------------------------------------------------------
r1170 | dahnke | 2017-08-30 18:59:05 +0200 (Wed, 30 Aug 2017) | 22 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
A  +    cat_io_volctype.m
M       cat_main.m
M       cat_main_registration.m
M       cat_surf_createCS.m
M       cat_surf_render2.m
M       cat_vol_iscaling.m
A       cat_vol_urqio.m
D       internal/cat_io_volctype.m
M       tbx_cfg_cat.m

(1) New:      Added function cat_vol_urqio to improve ultra-high resolution data
              (URQIO = Ultrahigh Resolution Quantitative Image Optimization) and
              added a GUI to control it.
              This function is still in development!
(2) Changed:  Improved cat_io_volctype and moved it to main directory.
(3) Fixed:    Small corrections in cat_surf_render2 and cat_vol_iscaling.
(4) Changed:  Added sharpening routine for cerebellar surface reconstruction and
              increase resolution parameter.

------------------------------------------------------------------------
r1169 | gaser | 2017-08-25 14:40:18 +0200 (Fri, 25 Aug 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       internal/correct_HCP_annot.m

Fixed: Changed name for HCP-MMP1 atlas to HCP_MMP1 because "-" is not
allowd for fieldnames.


------------------------------------------------------------------------
r1168 | gaser | 2017-08-25 14:39:42 +0200 (Fri, 25 Aug 2017) | 18 lines

Changed paths:
M       CHANGES.txt
D       atlases_surfaces/lh.aparc_HCP-MMP1.freesurfer.annot
        > moved to atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot
A  +    atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot
        > moved from atlases_surfaces/lh.aparc_HCP-MMP1.freesurfer.annot
D       atlases_surfaces/rh.aparc_HCP-MMP1.freesurfer.annot
        > moved to atlases_surfaces/rh.aparc_HCP_MMP1.freesurfer.annot
A  +    atlases_surfaces/rh.aparc_HCP_MMP1.freesurfer.annot
        > moved from atlases_surfaces/rh.aparc_HCP-MMP1.freesurfer.annot
M       cat_conf_stools.m
M       cat_surf_render2.m
M       cat_surf_results.m
MM      internal/correct_HCP_annot.m

Fixed: Changed name for HCP-MMP1 atlas to HCP_MMP1 because "-" is not
allowd for fieldnames.

------------------------------------------------------------------------
r1167 | gaser | 2017-08-25 14:11:25 +0200 (Fri, 25 Aug 2017) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_surf_render2.m
M       cat_surf_surf2roi.m

Changed: Added ROI support for Human Connectome Project (HCP) Multi-Modal
Parcellation for surfaces.


------------------------------------------------------------------------
r1166 | gaser | 2017-08-25 14:00:03 +0200 (Fri, 25 Aug 2017) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
A       atlases_surfaces/lh.aparc_HCP-MMP1.freesurfer.annot
A       atlases_surfaces/rh.aparc_HCP-MMP1.freesurfer.annot
M       cat_io_FreeSurfer.m
M       cat_surf_results.m
M       html/cat.html
A       internal/correct_HCP_annot.m

(1) Added: Human Connectome Project (HCP) Multi-Modal Parcellation for surfaces.
(2) Changed: Added option to suppress neg. (inverse) results for displaying
    surface results.
(3) Changed: Some cosmetic changes in cat_io_Freesurfer.m.

------------------------------------------------------------------------
r1165 | gaser | 2017-08-16 17:32:53 +0200 (Wed, 16 Aug 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_main_registration.m

Fixed: Prevent writing additional Dartel folder with xml-files if not necessary.

------------------------------------------------------------------------
r1164 | gaser | 2017-08-09 13:54:50 +0200 (Wed, 09 Aug 2017) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_run_job_APP_final.m

(1) Changed: Default non-linear registration is still DARTEL.
(2) Fixed: Typos


------------------------------------------------------------------------
r1163 | gaser | 2017-08-07 23:57:32 +0200 (Mon, 07 Aug 2017) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_surf_vol2surf.m
 M      internal/PAIL/pale_ui.fig
 M      internal/PAIL/pale_ui.m
 M      internal/PAIL/pale_ui_help.fig
 M      internal/PAIL/pale_ui_help.m
 M      internal/PAIL/spm_ov_pale.m

Changed: Added options for using offset and changed many options in
cat_surf_vol2surf.m and cat_conf_stools.m

------------------------------------------------------------------------
r1162 | dahnke | 2017-08-07 18:41:21 +0200 (Mon, 07 Aug 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_sanlm.m
M       ds.m
MM      internal/cat_vol_optimizeTemplate.m

(1) Fixed:    Corrected error in SANLM filter due to small values by adding an
              simple intensity normalization in cat_vol_sanlm.

------------------------------------------------------------------------
r1161 | dahnke | 2017-08-07 14:07:32 +0200 (Mon, 07 Aug 2017) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_sanlm.m
M       ds.m
A       internal/PAIL
A       internal/PAIL/pale_ui.fig
A       internal/PAIL/pale_ui.m
A       internal/PAIL/pale_ui_help.fig
A       internal/PAIL/pale_ui_help.m
A       internal/PAIL/spm_ov_pale.m

(1) New:      Added Point And Label setting Extension (PALE) orthview plugin
              to internal directory.
(2) Fixed:    Corrected error in optimised SANLM filter (cat_vol_sanlm).

------------------------------------------------------------------------
r1160 | gaser | 2017-08-07 11:15:37 +0200 (Mon, 07 Aug 2017) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_run_job1070.m
M       cat_surf_createCS.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Changed: Parameters for final deformable surface are now resulting in
    a smoother surface in cat_surf_createCS.m
(2) Changed: Updated help text.


------------------------------------------------------------------------
r1159 | dahnke | 2017-08-04 16:08:14 +0200 (Fri, 04 Aug 2017) | 46 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_opts.m
M       cat_defaults.m
M       cat_io_writenii.m
M       cat_main.m
M       cat_main_cleanup.m
M       cat_main_gintnorm.m
M       cat_main_registration.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_run_job_APP_SPM.m
M       cat_surf_display.m
M       cat_surf_info.m
M       cat_surf_render2.m
M       cat_vol_approx.m
M       cat_vol_div.m
M       cat_vol_smooth3X.m
M       html/images/cat_tst_seg_bwp_ana.png
A       internal/cat_vol_optimizeTemplate.m
M       tbx_cfg_cat.m

(1) Fixed:   Force one Gaussian per class in case of skull-stripped data to
             avoid segmentation errors.
(2) Fixed:   Corrected xy-flip error in cat_vol_div.
(3) Fixed:   Added cerebellum surface cases to cat_surf_info & cat_surf_display.
(4) Fixed:   Reduce strength of WM cleanup in cat_main_cleanup to reduce
             skull-stripping problems with missed brain.
(5) Fixed:   Corrected problems in case of different normalization and output
             resolution in cat_main_registration and cat_io_writenii.
(6) Changed: Modify registration option in the GUI to improve the handling of
             Dartel and Shooting registration. Added a Shooting template entry
             in the CAT_default file and moved the functions that find the
             Template images from cat_main to cat_run.
(7) Changed: Updated the SPM ngaus parameter in cat_defaults and added further
             comments.
(8) New:     Added internal script cat_vol_optimizeTemplate to optimise Dartel
             and Shooting templates.
(9) New:     Added developer GUI option for fast reconstruction of cerebrum and
             cerebellum that takes only seconds.




------------------------------------------------------------------------
r1158 | gaser | 2017-08-01 17:21:31 +0200 (Tue, 01 Aug 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_vol_div.m
M       html/cat.html

Changed: Divergence function in cat_vol_div.m was too memory demanding for
some systems.

------------------------------------------------------------------------
r1157 | gaser | 2017-08-01 14:06:13 +0200 (Tue, 01 Aug 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       html/cat.html

Fixed: Corrected print error for cortical thickness in cat_main.m

------------------------------------------------------------------------
r1156 | gaser | 2017-07-31 18:24:26 +0200 (Mon, 31 Jul 2017) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_vol_smooth3X.m
M       html/cat.html

(1) Fixed: Commands ismatrix|isrow|iscolumn are not working with older matlab
    versions.
(2) Fixed: Corrected index error in CAT_ConvexHull.c that caused crashes in
    CAT_FixTopology under windows.


------------------------------------------------------------------------
r1155 | gaser | 2017-07-17 20:26:55 +0200 (Mon, 17 Jul 2017) | 18 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_createCS.m
M       html/cat.html
 M      templates_animals/dog_T1.nii
 M      templates_animals/dog_Template_0.nii
 M      templates_animals/dog_Template_1.nii
 M      templates_animals/dog_Template_2.nii
 M      templates_animals/dog_Template_3.nii
 M      templates_animals/dog_Template_4.nii
 M      templates_animals/dog_Template_5.nii
 M      templates_animals/dog_Template_6.nii
 M      templates_animals/dog_brainmask.nii

Fixed: Forgot to correct flags for CAT_FixTopology in cat_surf_createCS.m


------------------------------------------------------------------------
r1154 | gaser | 2017-07-16 23:47:03 +0200 (Sun, 16 Jul 2017) | 28 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.fig
M       cat_amap.mexmaci64
M       cat_ornlm.mexmaci64
M       cat_sanlm.mexmaci64
M       cat_vbdist.mexmaci64
M       cat_vol_downcut.mexmaci64
M       cat_vol_eidist.mexmaci64
M       cat_vol_genus0.mexmaci64
M       cat_vol_gradient3.mexmaci64
M       cat_vol_interp3f.mexmaci64
M       cat_vol_laplace3.mexmaci64
M       cat_vol_laplace3R.mexmaci64
M       cat_vol_localstat.mexmaci64
M       cat_vol_median3.mexmaci64
M       cat_vol_median3c.mexmaci64
M       cat_vol_pbtp.mexmaci64
M       cat_vol_simgrow.mexmaci64
M       compile.m
M       html/cat.html
M       html/cat_tools_SBM.html
M       internal/cat_vol_cMRegularizarNLM3D.mexmaci64

Fixed: Use old version r1113 for CAT_FixTopology for windows because
of memory issues.

------------------------------------------------------------------------
r1153 | dahnke | 2017-07-05 17:40:07 +0200 (Wed, 05 Jul 2017) | 23 lines

Changed paths:
M       CHANGES.txt
M       templates_1.50mm/Template_0_IXI555_MNI152_GS.nii
M       templates_1.50mm/Template_1_IXI555_MNI152_GS.nii
M       templates_1.50mm/Template_2_IXI555_MNI152_GS.nii
M       templates_1.50mm/Template_3_IXI555_MNI152_GS.nii
M       templates_1.50mm/Template_4_IXI555_MNI152_GS.nii

Changed:  Updated the Shooting template by a 1.5 mm version of the IXI template
          processed with 1.0 mm and modified Shooting parameter with reduced
          decay of coarse to fine schedule
              lam = 1/3;  % default 0.5
          and adapted schedule parameter
              d.sched = (d.sched - d.sched(end)) / diff([d.sched(end), ...
                         d.sched(1)])*(inter-1)+1;
          rather than
              d.sched = d.sched/d.sched(end);
          to a similar spectrum of values with smoother changes to increase the
          amount of low frequency deformation and have smooth changes at all
          template stages. Keep in mind that even this template show much more
          anatomical details than the Dartel template, it requires less strong
          deformations to achieve this!

------------------------------------------------------------------------
r1152 | dahnke | 2017-07-05 14:28:08 +0200 (Wed, 05 Jul 2017) | 29 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_main.m
M       cat_main_gcut.m
M       cat_run_job.m
M       cat_run_job1070.m
M       cat_spm_preproc_run.m
M       cat_vol_morph.m
M       cat_vol_smooth3X.m
M       spm_cat12.m
A       templates_animals/dog_T1.nii
A       templates_animals/dog_Template_0.nii
A       templates_animals/dog_Template_1.nii
A       templates_animals/dog_Template_2.nii
A       templates_animals/dog_Template_3.nii
A       templates_animals/dog_Template_4.nii
A       templates_animals/dog_Template_5.nii
A       templates_animals/dog_Template_6.nii
A       templates_animals/dog_brainmask.nii

(1) Fixed:   Corrected problems of the lower intensity boundary in images with
             high intensity background (R1, MP2Rage) in rough APP pipeline
             (r1070).
(2) New:     Prepared preprocessing of dogs.
(3) Fixed:   Corrected error in primate processing by removing the msk field.
(4) Changed: Small changes in cat_vol_smooth3X.
(5) Changed: Removed warning in cat_vol_morph that confuse the users.

------------------------------------------------------------------------
r1151 | gaser | 2017-07-03 00:32:37 +0200 (Mon, 03 Jul 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       Makefile

Changed: Updated Makefile


------------------------------------------------------------------------
r1150 | gaser | 2017-07-03 00:31:14 +0200 (Mon, 03 Jul 2017) | 9 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_vol_groupwise_ls.m

Changed: Updated CAT12 manual w.r.t. longitudinal processing.

------------------------------------------------------------------------
r1149 | dahnke | 2017-06-23 12:31:47 +0200 (Fri, 23 Jun 2017) | 27 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main.m
M       cat_run_job.m
M       cat_run_job_APP_SPM.m
M       cat_surf_createCS.m
M       cat_vol_approx.m
M       cat_vol_partvol.m
M       html/images/cat_tst_seg_bwp_ana.png

(1) Fixed:   Corrected error in cat_run_job_SPM head threshold estimation.
(2) New:     Added detection of high intensity background in cat_run_job_SPM
             to improve correction of MP2Rage and R1 protocols.
(3) New:     Added old cleanup option in Expert GUI.
(4) New:     Added enhanced skull-stripping/cleanup for SPM segmentation for R1
             and MP2Rage images.
(5) Changed: Modified APP1 and APP2 SPM bias correction parameter in cat_run_job
             and use the SPM affine registration for initial registration
(6) Changed: Updated cat_run_job_APP_SPM to improve performance in case of
             R1, MT, and MP2Rage data.
(7) Changed: Added background condition (at least CSF) before interpolation and
             optimised median filter for Yppi correction in cat_surf_createCS.
(8) Fixed:   Corrected nan-error in cat_vol_approx.
(9) Changed: Modify blood-vessel correction in cat_vol_partvol to reduce
             skull-stripping problems.

------------------------------------------------------------------------
r1148 | gaser | 2017-06-22 10:43:56 +0200 (Thu, 22 Jun 2017) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_oldcatch.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Fixed: Repcaed nanmean by cat_stat_nanmean
(2) Fixed: Correct call to cat_run_jobX for older matlab versions
(3) Chnaged: Force running in foreground if only one processor is found

------------------------------------------------------------------------
r1147 | gaser | 2017-06-21 11:31:53 +0200 (Wed, 21 Jun 2017) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
MM      cat_run_job1070.m
MM      cat_run_job_APP_init1070.m
M       html/cat.html
M       html/cat_methods_validation.html
M       html/cat_tools_SBM.html

Changed: Updated html help.

------------------------------------------------------------------------
r1146 | gaser | 2017-06-21 11:20:11 +0200 (Wed, 21 Jun 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       html/cat.html
M       tbx_cfg_cat.m

Changed: Updated menus in GUI.

------------------------------------------------------------------------
r1145 | dahnke | 2017-06-20 14:18:59 +0200 (Tue, 20 Jun 2017) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_run_job.m
A       cat_run_job1070.m
M       cat_run_job_APP_SPM.m
A       cat_run_job_APP_init1070.m
M       cat_run_newcatch.m
M       cat_vol_approx.m

(1) Changed:  Added "cat_run_job1070" and "cat_run_job_APP_init1070", update the
              GUI and set it as default APP preprocessing.
(2) Changed:  Removed last changes in "cat_main_LAS" of calling "cat_vol_approx"
              with automatic smoothness constrain that did not work yet.

------------------------------------------------------------------------
r1144 | dahnke | 2017-06-19 17:04:18 +0200 (Mon, 19 Jun 2017) | 29 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_opts.m
M       cat_defaults.m
M       cat_io_report.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job_APP_SPM.m
M       cat_run_job_APP_init.m
M       cat_spm_preproc_run.m
M       cat_tst_qa.m
M       cat_vol_approx.m
M       cat_vol_div.m
M       cat_vol_grad.m
M       html/images/cat_tst_seg_bwp_ana.png

(1) Changed:  Changed APP1 and APP2 SPM parameter for faster processing.
(2) Changed:  Use lower resolution (1.0 mm) only in case of data with <0.8 mm
              average voxel size.
(3) Changed:  Added mark2rps equation to QA XML.
(4) Changed:  Removed sanlm variable and added options to NCstr variable.
(5) Changed:  Corrected small errors.
(6) Changed:  Used automatic LASstr modification parameter.
(7) Changed:  Refined tissue handling in APP_SPM function.


------------------------------------------------------------------------
r1143 | gaser | 2017-06-14 12:55:48 +0200 (Wed, 14 Jun 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       Makefile
MM      cat_stat_polynomial.m

Changed: Added function to only scp CAT12-Manual to dbm.

------------------------------------------------------------------------
r1142 | gaser | 2017-06-14 12:50:45 +0200 (Wed, 14 Jun 2017) | 9 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       html/cat_starting.html

Changed: Updated CAT12 manual and added more information and images for
defining contrasts.

------------------------------------------------------------------------
r1141 | gaser | 2017-06-14 08:40:45 +0200 (Wed, 14 Jun 2017) | 7 lines

Changed paths:
M       CHANGES.txt
A       cat_stat_polynomial.m

Added: cat_stat_polynomial for polynomial expansion and orthogonalization
of a function.

------------------------------------------------------------------------
r1140 | gaser | 2017-06-13 11:21:16 +0200 (Tue, 13 Jun 2017) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_resamp.m
M       templates_surfaces/lc.central.Template_T1_IXI555_MNI152.gii
M       templates_surfaces/lc.central.freesurfer.gii
M       templates_surfaces/lc.sphere.freesurfer.gii
M       templates_surfaces/rc.central.Template_T1_IXI555_MNI152.gii
M       templates_surfaces/rc.central.freesurfer.gii
M       templates_surfaces/rc.sphere.freesurfer.gii

Changed: Temporarily written files during resampling & Smoothing now have
unique names.

------------------------------------------------------------------------
r1139 | gaser | 2017-06-12 21:54:51 +0200 (Mon, 12 Jun 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_opts.m
M       cat_io_cgw2seg.m
M       cat_main.m

Fixed: Typos...

------------------------------------------------------------------------
r1138 | dahnke | 2017-06-12 16:26:32 +0200 (Mon, 12 Jun 2017) | 29 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_opts.m
M       cat_defaults.m
M       cat_run.m
M       cat_run_job.m
MM      cat_run_job_APP_SPM.m
M       cat_run_job_APP_init.m
MM      cat_spm_preproc_run.m
MM      cat_spm_smoothto8bit.m
M       html/images/cat_tst_seg_bwp_ana.png
M       tbx_cfg_cat.m

(1) Changed:   Large changes in cat_run_job to simplify APP cases
                * APP=0 - do nothing
                * APP=1 - use SPM bias correction
                * APP=2 - use SPM + APPs bias correction
                * APP=3 - APP init (old APP1)
                * APP=4 - APP final
               and to improve behaviour in case of skull-stripped data:
                * Added TPM update that combine head and background classes to
                  one background class in cat_run_job.
                * Added noise to the background to guarantee SPM requirements
                  of gaussian distributed data in cat_run_job.
                * Added
(2) Changed:   Update GUI changing the *str parameters from real data input to
               fix cases.

------------------------------------------------------------------------
r1137 | dahnke | 2017-06-11 20:00:39 +0200 (Sun, 11 Jun 2017) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_LAS.m
M       cat_main_gcut.m
M       cat_main_gintnorm.m
M       cat_surf_createCS.m

(1) Changed:    Deactivated closing of small WMHs in cat_vol_createCS and
                prepared fast surface generation to check segmentation.
(2) Changed:    Updated SPM skull-stripping and fast surface output in cat_main.
(3) Changed:    Increased upper WM threshold in cat_main_gcut.
(4) Changed:    Corrected problems in cat_main_LAS for MP2RAGE protocols.




------------------------------------------------------------------------
r1136 | dahnke | 2017-06-11 16:04:58 +0200 (Sun, 11 Jun 2017) | 25 lines

Changed paths:
M       CHANGES.txt
M       cat_io_cgw2seg.m
M       cat_plot_boxplot.m
A       cat_run_job_APP_SPM.m
A       cat_spm_preproc_run.m
A       cat_spm_smoothto8bit.m
M       cat_surf_info.m
M       cat_surf_render2.m
M       cat_tst_calc_kappa.m
M       cat_tst_qa.m
M       cat_vol_div.m
M       cat_vol_grad.m
M       cat_vol_resize.m
M       ds.m
M       internal/cat_vol_flipside.m
 M      templates_1.50mm

(1) New:        Added surface rendering for Matlab surface in cat_surf_render2.
(2) New:        Added label map generation for FS input in cat_io_cgw2seg.
(3) Changed :   Updated cat_tst_calc_kappa to process slice segments with more
                than one class and correct Kappa estimation in case of multiple
                classes.
(4) Changed:    Small independent corrections in other functions.

------------------------------------------------------------------------
r1135 | gaser | 2017-06-07 11:04:11 +0200 (Wed, 07 Jun 2017) | 25 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat12.fig
A  +    cat_batch_cat.m
        > moved from cat_batch_vbm.m
A  +    cat_batch_cat.sh
        > moved from cat_batch_vbm.sh
M       cat_batch_long.sh
M       cat_batch_spm.sh
D       cat_batch_vbm.m
        > moved to cat_batch_cat.m
D       cat_batch_vbm.sh
        > moved to cat_batch_cat.sh
M       cat_io_senderrormail.m
M       cat_surf_results.m
M       html/cat_methods_RBM.html
M       html/cat_starting.html

(1) Changed: Updated online help text and manual.
(2) Fixed: Corrected estimate of currect directory in bash scripts (thanks to
    Markus Mertens for pointing to that error).
(3) Changed: renamed batch scripts for CAT.

------------------------------------------------------------------------
r1134 | gaser | 2017-05-31 15:45:42 +0200 (Wed, 31 May 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_surf_createCS.m

Changed: SPM.mat in cat12 is now always saved with -v7.3 flag to prevent issues
with large files.


------------------------------------------------------------------------
r1133 | gaser | 2017-05-23 10:55:55 +0200 (Tue, 23 May 2017) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_install_atlases.m
 M      templates_surfaces/lc.central.Template_T1_IXI555_MNI152.gii
 M      templates_surfaces/lc.central.freesurfer.gii
 M      templates_surfaces/lc.sphere.freesurfer.gii
 M      templates_surfaces/lc.thickness.Template_T1_IXI555_MNI152
 M      templates_surfaces/rc.central.Template_T1_IXI555_MNI152.gii
 M      templates_surfaces/rc.central.freesurfer.gii
 M      templates_surfaces/rc.sphere.freesurfer.gii
 M      templates_surfaces/rc.thickness.Template_T1_IXI555_MNI152

(1) Changed: Atlas installation function will now install all available
    atlases and not only those that are set in cat_defaults.m.

------------------------------------------------------------------------
r1132 | gaser | 2017-05-23 10:29:27 +0200 (Tue, 23 May 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       templates_surfaces/lc.thickness.Template_T1_IXI555_MNI152
M       templates_surfaces/rc.thickness.Template_T1_IXI555_MNI152

(1) Changed: Updated cerebellar thickness files.

------------------------------------------------------------------------
r1131 | gaser | 2017-05-22 17:06:39 +0200 (Mon, 22 May 2017) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m
A       templates_surfaces/lc.central.Template_T1_IXI555_MNI152.gii
A       templates_surfaces/lc.central.freesurfer.gii
A       templates_surfaces/lc.sphere.freesurfer.gii
A       templates_surfaces/lc.thickness.Template_T1_IXI555_MNI152
A       templates_surfaces/rc.central.Template_T1_IXI555_MNI152.gii
A       templates_surfaces/rc.central.freesurfer.gii
A       templates_surfaces/rc.sphere.freesurfer.gii
A       templates_surfaces/rc.thickness.Template_T1_IXI555_MNI152

(1) Added: Added cerebellar template.
(2) Changed: Added spherical registration to cerebellar template.

------------------------------------------------------------------------
r1130 | gaser | 2017-05-22 14:57:16 +0200 (Mon, 22 May 2017) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_main.m
M       cat_run.m
M       cat_surf_createCS.m
M       tbx_cfg_cat.m

(1) Changed: Added preliminary surface processing of cerebellar hemispheres
    (experimental!).
(2) Changed: Number of gaussian curves for initial SPM12 segmentation was
    changed.

------------------------------------------------------------------------
r1129 | gaser | 2017-05-09 14:58:31 +0200 (Tue, 09 May 2017) | 7 lines

Changed paths:
M       CHANGES.txt
MM      cat_stat_diff.m
M       cat_vol_ctype.m

Fixed: Issue with integers in cat_vol_ctype.m on older matlab versions.

------------------------------------------------------------------------
r1128 | gaser | 2017-05-05 10:37:51 +0200 (Fri, 05 May 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_run_job.m
M       cat_vol_ctype.m

Fixed: Solved some compatibility issues with windows.

------------------------------------------------------------------------
r1127 | gaser | 2017-05-05 09:49:49 +0200 (Fri, 05 May 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat12.fig
A       cat_stat_diff.m
M       kmeans3D.m

Added: Tool for calculating differences between multiple images or surfaces.

------------------------------------------------------------------------
r1126 | gaser | 2017-04-21 17:06:58 +0200 (Fri, 21 Apr 2017) | 38 lines

Changed paths:
M       CHANGES.txt
!       cat_amap.mexglx
M       cat_amap.mexw32
!       cat_ornlm.mexglx
M       cat_ornlm.mexw32
!       cat_sanlm.mexglx
M       cat_sanlm.mexw32
!       cat_vbdist.mexglx
M       cat_vbdist.mexw32
!       cat_vol_downcut.mexglx
M       cat_vol_downcut.mexw32
!       cat_vol_eidist.mexglx
M       cat_vol_eidist.mexw32
!       cat_vol_eikonal3.mexglx
!       cat_vol_genus0.mexglx
M       cat_vol_genus0.mexw32
!       cat_vol_gradient3.mexglx
M       cat_vol_gradient3.mexw32
!       cat_vol_interp3f.mexglx
M       cat_vol_interp3f.mexw32
!       cat_vol_laplace3.mexglx
M       cat_vol_laplace3.mexw32
!       cat_vol_laplace3R.mexglx
M       cat_vol_laplace3R.mexw32
!       cat_vol_localstat.mexglx
M       cat_vol_localstat.mexw32
!       cat_vol_median3.mexglx
M       cat_vol_median3.mexw32
!       cat_vol_median3c.mexglx
M       cat_vol_median3c.mexw32
!       cat_vol_pbtp.mexglx
M       cat_vol_pbtp.mexw32
!       cat_vol_simgrow.mexglx
M       cat_vol_simgrow.mexw32

Fixed: Compiled for 32bit Windows.

------------------------------------------------------------------------
r1125 | gaser | 2017-04-21 16:45:00 +0200 (Fri, 21 Apr 2017) | 50 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_amap.mexa64
M       cat_amap.mexw64
M       cat_ornlm.mexa64
M       cat_ornlm.mexw64
M       cat_sanlm.mexa64
M       cat_sanlm.mexw64
MM      cat_spm_affreg.m
M       cat_vbdist.mexa64
M       cat_vbdist.mexw64
M       cat_vol_downcut.mexa64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.mexa64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.c
M       cat_vol_genus0.mexa64
M       cat_vol_genus0.mexmaci64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mexa64
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mexa64
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.mexa64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mexa64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexa64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexa64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexa64
M       cat_vol_median3c.mexw64
M       cat_vol_pbtp.mexa64
M       cat_vol_pbtp.mexw64
M       cat_vol_simgrow.mexa64
M       cat_vol_simgrow.mexw64
M       html/cat.html
 M      html/images/cat_tst_seg_bwp_boxplot_para_CAT.png
 M      html/images/cat_tst_seg_bwp_boxplot_para_SPM.png
 M      html/images/cat_tst_seg_exp_boxplot_para_CAT.png
 M      html/images/cat_tst_seg_exp_boxplot_para_SPM.png
 M      html/images/cat_tst_seg_ibsr_boxplot.png
 M      html/images/cat_tst_seg_ibsr_detail.png
 M      html/images/cat_tst_seg_sve_detail.png

Changed: Added 2nd run to genus0 approach with different parameters to obtain
better topology correction.

------------------------------------------------------------------------
r1124 | dahnke | 2017-04-05 16:35:35 +0200 (Wed, 05 Apr 2017) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_registration.m
M       compile.m

(1) Changed:    Force to use odd image dimension for normalized image dimension
                in cat_main_registration (thanks to Xirui Hou for pointing out
                this issue).
(2) Fixed:      Corrected voxel dimension of the transformation and Jacobian
                determinant (thanks to Gabriel Ziegler and Felix Hoffstaedter).

------------------------------------------------------------------------
r1123 | gaser | 2017-04-04 15:02:58 +0200 (Tue, 04 Apr 2017) | 27 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cat_amap.mexmaci64
M       cat_conf_extopts.m
M       cat_ornlm.mexmaci64
M       cat_sanlm.mexmaci64
M       cat_vbdist.mexmaci64
M       cat_vol_downcut.mexmaci64
M       cat_vol_eidist.mexmaci64
M       cat_vol_genus0.mexmaci64
M       cat_vol_gradient3.mexmaci64
M       cat_vol_interp3f.mexmaci64
M       cat_vol_laplace3.mexmaci64
M       cat_vol_laplace3R.mexmaci64
M       cat_vol_localstat.mexmaci64
M       cat_vol_median3.mexmaci64
M       cat_vol_median3c.mexmaci64
M       cat_vol_pbtp.mexmaci64
M       cat_vol_simgrow.mexmaci64
M       compile.m
M       internal/cat_vol_cMRegularizarNLM3D.mexmaci64
M       kmeans3D.m

(1) Fixed: Added kmeans3D.m to distribution
(2) Changed: Changed path of compilation to pwd

------------------------------------------------------------------------
r1122 | dahnke | 2017-04-03 19:09:48 +0200 (Mon, 03 Apr 2017) | 106 lines

Changed paths:
M       CHANGES.txt
M       cat_amap.mexmaci64
M       cat_conf_extopts.m
M       cat_conf_opts.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_main_gintnorm.m
M       cat_main_registration.m
M       cat_ornlm.mexmaci64
M       cat_plot_boxplot.m
M       cat_run_job.m
M       cat_sanlm.mexmaci64
A       cat_spm_affreg.m
M       cat_stat_nanmean.m
M       cat_stat_nanstd.m
M       cat_stat_nansum.m
M       cat_tst_calc_kappa.m
M       cat_tst_qa.m
M       cat_vbdist.mexmaci64
M       cat_vol_downcut.mexmaci64
M       cat_vol_eidist.mexmaci64
M       cat_vol_genus0.mexmaci64
M       cat_vol_gradient3.mexmaci64
M       cat_vol_laplace3.mexmaci64
M       cat_vol_laplace3R.mexmaci64
M       cat_vol_localstat.mexmaci64
M       cat_vol_median3.mexmaci64
M       cat_vol_median3c.mexmaci64
M       cat_vol_morph.m
M       cat_vol_partvol.m
M       cat_vol_simgrow.mexmaci64
M       compile.m
M       html/cat_methods_validation.html
M       html/images/cat_tst_seg_BWP_boxplot.png
M       html/images/cat_tst_seg_BWP_detail.png
M       html/images/cat_tst_seg_bwp_ana.png
M       html/images/cat_tst_seg_bwp_boxplot_para.png
D       html/images/cat_tst_seg_bwp_boxplot_para_APP.png
A       html/images/cat_tst_seg_bwp_boxplot_para_CAT.png
D       html/images/cat_tst_seg_bwp_boxplot_para_CU.png
D       html/images/cat_tst_seg_bwp_boxplot_para_LAS.png
D       html/images/cat_tst_seg_bwp_boxplot_para_LC.png
D       html/images/cat_tst_seg_bwp_boxplot_para_NLM.png
A       html/images/cat_tst_seg_bwp_boxplot_para_SPM.png
D       html/images/cat_tst_seg_bwp_boxplot_para_SR.png
D       html/images/cat_tst_seg_bwp_boxplot_para_SS.png
D       html/images/cat_tst_seg_bwp_boxplot_para_WR.png
D       html/images/cat_tst_seg_bwp_boxplot_para_aff.png
D       html/images/cat_tst_seg_bwp_boxplot_para_bf.png
D       html/images/cat_tst_seg_bwp_boxplot_para_breg.png
D       html/images/cat_tst_seg_bwp_boxplot_para_ng.png
D       html/images/cat_tst_seg_bwp_boxplot_para_other.png
D       html/images/cat_tst_seg_bwp_boxplot_para_res.png
M       html/images/cat_tst_seg_bwp_detail_para.png
M       html/images/cat_tst_seg_exp_boxplot.png
D       html/images/cat_tst_seg_exp_boxplot_para.png
D       html/images/cat_tst_seg_exp_boxplot_para_APP.png
A       html/images/cat_tst_seg_exp_boxplot_para_CAT.png
D       html/images/cat_tst_seg_exp_boxplot_para_CU.png
D       html/images/cat_tst_seg_exp_boxplot_para_LAS.png
D       html/images/cat_tst_seg_exp_boxplot_para_LC.png
D       html/images/cat_tst_seg_exp_boxplot_para_NLM.png
A       html/images/cat_tst_seg_exp_boxplot_para_SPM.png
D       html/images/cat_tst_seg_exp_boxplot_para_SR.png
D       html/images/cat_tst_seg_exp_boxplot_para_SS.png
D       html/images/cat_tst_seg_exp_boxplot_para_WR.png
D       html/images/cat_tst_seg_exp_boxplot_para_aff.png
D       html/images/cat_tst_seg_exp_boxplot_para_bf.png
D       html/images/cat_tst_seg_exp_boxplot_para_breg.png
D       html/images/cat_tst_seg_exp_boxplot_para_ng.png
D       html/images/cat_tst_seg_exp_boxplot_para_other.png
D       html/images/cat_tst_seg_exp_boxplot_para_res.png
M       html/images/cat_tst_seg_exp_detail.png
M       html/images/cat_tst_seg_exp_detail_para.png
A       html/images/cat_tst_seg_ibsr_boxplot.png
A       html/images/cat_tst_seg_ibsr_detail.png
M       html/images/cat_tst_seg_sve_boxplot.png
A       html/images/cat_tst_seg_sve_detail.png

(1)  New:        Added detection of skull-stripped data to improve the affine
                 registration in cat_run_job. For initial affine registration a
                 brain mask is applied to the template. Furthermore, the number
                 of gaussian classes is corrected and checkt after the first
                 SPM preprocessing.
(2)  New:        If the initial affine registration failed and the AC is outside
                 of the image, than the COM is used to reinitialise the the
                 registration (cat_run_job).
(3)  New:        Added biasfwhm modifier in case of strong inhomogeneities in
                 cat_run_job.
(4)  Changed:    Refined the fine affine registration in cat_run_job by further
                 steps to reduce problems in R1 weighted scans and skull-striped
                 data. In case of skull-stripped data the brain mask is used.
(4)  Changed:    Added cat_spm_affreg to avoid popup error message in case of
                 initial affine registration errors that are maybe fixed by
                 COM initialisation or spm_maff8.
(5)  Changed:    Removed affreg case 'subj' regularisation because the results
                 were equivalent with the case 'none' registration.
                 Added comments for some parameter in cat_conf_opts.
(6)  Fixed:      Corrected problems in cat_main_gintnorm and cat_main_LAS for
                 inverse contrasts.
(7)  Fixed:      Corrected handling of template cases in cat_main_registration.
(8)  Fixed:      Replaced mean by cat_stat_nanmean in cat_tst_qa.
(9)  Changed:    Added grouping (gray background blocks) in cat_plot_boxplot.


------------------------------------------------------------------------
r1121 | gaser | 2017-03-31 08:54:16 +0200 (Fri, 31 Mar 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_long_APP.m
M       html/cat.html

Fixed: Initialization of APP for longitudinal batch mode was incorrect.

------------------------------------------------------------------------
r1120 | gaser | 2017-03-21 11:01:35 +0100 (Tue, 21 Mar 2017) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_conf_stools.m
M       cat_main.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Changed: Updated help text.
(2) Fixed: WMH volume estimation was not related to voxel size.
(3) Fixed: Surface flag for cat_surf_display.m in cat_main.m was not correct.
(4) Changed: Updated output and display in cat_main.m (range of thickness,
    cm^3,...)

------------------------------------------------------------------------
r1119 | gaser | 2017-03-20 17:00:39 +0100 (Mon, 20 Mar 2017) | 35 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_surf_createCS.m
M       html/cat.html
M       html/cat_methods_validation.html
 M      html/images/cat_tst_reg_boxplot.png
 M      html/images/cat_tst_seg_bwp_ana.png
 M      html/images/cat_tst_seg_bwp_boxplot_para_APP.png
 M      html/images/cat_tst_seg_bwp_boxplot_para_CU.png
 M      html/images/cat_tst_seg_bwp_boxplot_para_SR.png
 M      html/images/cat_tst_seg_bwp_boxplot_para_WR.png
 M      html/images/cat_tst_seg_bwp_boxplot_para_aff.png
 M      html/images/cat_tst_seg_bwp_boxplot_para_bf.png
 M      html/images/cat_tst_seg_bwp_boxplot_para_breg.png
 M      html/images/cat_tst_seg_bwp_boxplot_para_ng.png
 M      html/images/cat_tst_seg_bwp_detail_para.png
 M      html/images/cat_tst_seg_exp_boxplot_para_SR.png
 M      html/images/cat_tst_seg_exp_boxplot_para_WR.png
 M      html/images/cat_tst_seg_exp_boxplot_para_aff.png
 M      html/images/cat_tst_seg_exp_boxplot_para_bf.png
 M      html/images/cat_tst_seg_exp_boxplot_para_breg.png
 M      html/images/cat_tst_seg_exp_boxplot_para_ng.png
 M      html/images/cat_tst_seg_sve_boxplot.png
 M      html/images/neonates.png

(1) Changed: Added option for initial morphological closing in the parahippocampal
    area to minimize large cuts after topology correction.
(2) Changed: Updated CAT_FixTo�ology to better deal with large topology aretefacts
(2) Changed: Updated help text.

------------------------------------------------------------------------
r1118 | gaser | 2017-03-17 16:57:00 +0100 (Fri, 17 Mar 2017) | 28 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_opts.m
M       cat_defaults.m
M       cat_io_cprintf.m
M       cat_main_LAS.m
M       cat_main_LASs.m
M       cat_main_registration.m
M       cat_plot_boxplot.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job_APP_final.m
M       cat_run_job_APP_init.m
M       cat_surf_createCS.m
M       cat_tst_cattest.m
M       cat_tst_qa_cleaner.m
M       cat_vol_correct_slice_scaling.m
M       cat_vol_pbt.m
M       cat_vol_sanlm.m
M       compile.m
M       html/cat_FAQ.html
M       html/cat_introduction.html
M       html/cat_methods_RBM.html
M       html/cat_methods_validation.html
M       html/cat_starting_cattest.html

Changed: Updated help text and corrected typos.

------------------------------------------------------------------------
r1117 | dahnke | 2017-03-16 16:31:20 +0100 (Thu, 16 Mar 2017) | 147 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_opts.m
M       cat_defaults.m
M       cat_io_writenii.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_main_cleanup.m
M       cat_main_gintnorm.m
M       cat_main_registration.m
M       cat_plot_boxplot.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job_APP_init.m
M       cat_surf_createCS.m
M       cat_surf_smooth.m
M       cat_tst_calc_kappa.m
M       cat_tst_qa.m
M       cat_vol_approx.m
M       cat_vol_findfiles.m
M       cat_vol_morph.m
M       cat_vol_partvol.m
M       cat_vol_pbt.m
M       cat_vol_sanlm.m
M       compile.m
M       html/cat.html
M       html/cat.txt
M       html/cat_FAQ.html
M       html/cat_methods_validation.html
M       html/images/CAT_PBT_for_SPM.png
A       html/images/cat_tst_reg_boxplot.png
M       html/images/cat_tst_seg_BWP_boxplot.png
M       html/images/cat_tst_seg_BWP_detail.png
A       html/images/cat_tst_seg_bwp_ana.png
A       html/images/cat_tst_seg_bwp_boxplot_para.png
A       html/images/cat_tst_seg_bwp_boxplot_para_APP.png
A       html/images/cat_tst_seg_bwp_boxplot_para_CU.png
A       html/images/cat_tst_seg_bwp_boxplot_para_LAS.png
A       html/images/cat_tst_seg_bwp_boxplot_para_LC.png
A       html/images/cat_tst_seg_bwp_boxplot_para_NLM.png
A       html/images/cat_tst_seg_bwp_boxplot_para_SR.png
A       html/images/cat_tst_seg_bwp_boxplot_para_SS.png
A       html/images/cat_tst_seg_bwp_boxplot_para_WR.png
A       html/images/cat_tst_seg_bwp_boxplot_para_aff.png
A       html/images/cat_tst_seg_bwp_boxplot_para_bf.png
A       html/images/cat_tst_seg_bwp_boxplot_para_breg.png
A       html/images/cat_tst_seg_bwp_boxplot_para_ng.png
A       html/images/cat_tst_seg_bwp_boxplot_para_other.png
A       html/images/cat_tst_seg_bwp_boxplot_para_res.png
A       html/images/cat_tst_seg_bwp_detail_para.png
A       html/images/cat_tst_seg_exp_boxplot.png
A       html/images/cat_tst_seg_exp_boxplot_para.png
A       html/images/cat_tst_seg_exp_boxplot_para_APP.png
A       html/images/cat_tst_seg_exp_boxplot_para_CU.png
A       html/images/cat_tst_seg_exp_boxplot_para_LAS.png
A       html/images/cat_tst_seg_exp_boxplot_para_LC.png
A       html/images/cat_tst_seg_exp_boxplot_para_NLM.png
A       html/images/cat_tst_seg_exp_boxplot_para_SR.png
A       html/images/cat_tst_seg_exp_boxplot_para_SS.png
A       html/images/cat_tst_seg_exp_boxplot_para_WMH.png
A       html/images/cat_tst_seg_exp_boxplot_para_WR.png
A       html/images/cat_tst_seg_exp_boxplot_para_aff.png
A       html/images/cat_tst_seg_exp_boxplot_para_bf.png
A       html/images/cat_tst_seg_exp_boxplot_para_breg.png
A       html/images/cat_tst_seg_exp_boxplot_para_ng.png
A       html/images/cat_tst_seg_exp_boxplot_para_other.png
A       html/images/cat_tst_seg_exp_boxplot_para_res.png
A       html/images/cat_tst_seg_exp_detail.png
A       html/images/cat_tst_seg_exp_detail_para.png
D       html/images/cat_tst_seg_real_boxplot.png
D       html/images/cat_tst_seg_real_detail.png
A       html/images/cat_tst_seg_sve_boxplot.png
A       html/images/neonates.png
M       html/style.css
M       internal/cat_vol_flipside.m

== New ==
(1) New*:      Added processing of images with BG<GM<WM<CSF contrast (neonates)
               as separate case that does not influence the default pipeline.
(2) New:       Added further preliminary validation results figures that are not
               linked in the help.

== Parameterupdates ==
(1) Changed:   opt.ngauss:
               Updated SPM ngauss parameter in cat_defaults with only one
               rather than three GM and WM classes because it was more stable
               onthe BWP and real Datasets.  More than one GM and WM gaussian
               peaks seams to bet better in case of inverse data (T2/PD).
               Hence, an automatically switch to more than three GM and WM
               peaks is added in the cat_run_job.
(2) Changed:   extopts.resval & extopts.restype:
               Increased the upper limit of the internal interpolation to 0.5 mm
               rather than 1.0 mm (resval = [0.5 0.3]) and add 1.0 mm as minimum
               resolution to improve the results in case of anisotropic high-
               resolution data (e.g., 0.5x0.5x1.5 mm) but also of low resolution
               data of the default interpolation option (restype = 'best').
(3) Changed:   opt.biasreg, opt.biasfwhm & opt.biasstr:
               Added opts.biasstr parameter to the cat_default-file and to
               the GUI to have a simple control parameter for inhomogeneity
               correction that controls the SPM preprocessing parameter
               opts.biasreg and opts.biasfwhm that were removed at once
               from the expert GUI.
(4) Changed:   Corrected LASstr parameter to give optimal results for 0.5.
(5) Changed:   opts.warpreg:
               Removed opts.warpreg parameter from expert GUI because our test
               indicated no useful changes with no general effects and only
               worse results in single cases.
(6) Changed:   Added additional sub parameter for lab operation in cat_vol_morph
               to allow more than one large cluster.


== Other Updates ==
(1) Changed:   Replace old SPM tissue threshold estimation by the @-function
               "clsint" in cat_main, cat_main_gintnorm.
(2) Changed:   Added transparency and saturation parameter to cat_plot_boxplot.
(3) Changed:   Forced low change rate for first Shooting template to improve
               Shooting quality of lower regstr values.
(4) Changed:   Added resolution dependency for cleanup of the initial SPM
               segmentation to avoid problems in case of low resolution.

(5) Changed:   Use realignment in "cat_tst_calc_kappa" in case of different
               resolution only if realign parameter is true. Otherwise, imcalc
               is used directly.
(6) Changed:   Updated help texts in cat_conf_opts and reduce the amount of
               control parameters.
(7) Changed:   Added resolution dependency in cat_vol_sanlm to reduce the amout
               of filtering in low resolution data.


== Bug fixes ==
(1) Fixed:     Corrected bugs in cat_run_APP_init.
(2) Fixed:     Corrected Ym intensity scaling problem in cat_main_LAS.
(3) Fixed:     Corrected index error in cat_surf_smooth.
               Thanks to Bj�rn Horing for pointing out this bug.
(4) Fixed:     Corrected WMH volume output in CAT report and XML file.
               Thanks to M.H.T. Zwartbol for pointing out this bug.
(5) Fixed:     Corrected simultan output of modulated data in expert mode in
               cat_io_writenii and cat_main.
               Thanks to Felix Hoffstaedter for pointing out this limitation.
(6) Fixed:     Corrected typo in SPM PBT figure.
(7) Fixed:     Special case in PBT data processing of binary data.





------------------------------------------------------------------------
r1116 | gaser | 2017-03-12 23:57:15 +0100 (Sun, 12 Mar 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m

Changed: Added option for additional 2D laplace filtering to topology
correction to minimize irregularities in coordinate maps for SPH.

------------------------------------------------------------------------
r1115 | gaser | 2017-03-10 09:49:11 +0100 (Fri, 10 Mar 2017) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_plot_boxplot.m
M       cat_stat_check_cov.m
M       cat_surf_createCS.m

(1) Changed: Parameter for topology corrections are slightly changed to force filling.
(2) Fixed: Some smaller errors in cat_stat_check_cov.m for surfaces.

------------------------------------------------------------------------
r1114 | gaser | 2017-03-02 11:46:01 +0100 (Thu, 02 Mar 2017) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.fig
M       cat_batch_long.m
M       cat_conf_long.m
M       cat_long_main.m
M       cat_long_multi_run.m
M       cat_surf_results.m
M       html/cat.html
M       tbx_cfg_cat.m

Changed: Added option to save deformations in longitudinal pipeline (useful for
applying the deformations to coregistered data).

------------------------------------------------------------------------
r1113 | gaser | 2017-03-01 15:43:36 +0100 (Wed, 01 Mar 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_createCS.m
M       html/cat.html

(1) Changed: Removed Convexity Smoothing in cat_surf_createCS.m that wasn't an
    improvement for many data.

------------------------------------------------------------------------
r1112 | gaser | 2017-02-24 12:13:25 +0100 (Fri, 24 Feb 2017) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_stat_spm2x.m
M       cat_surf_results.m

(1) Changed: APP is now disabled by default, because for "normal" data there
    seems to be no improvement. Use that option if something fails with your
    initial affine registration.
(2) Changed: Some minor changes in help text.
(3) Fixed: Check for surface files in cat_stat_spm2x.m

------------------------------------------------------------------------
r1111 | gaser | 2017-02-15 12:41:08 +0100 (Wed, 15 Feb 2017) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_cva_ui.m
M       cat_stat_spm2x.m
M       cat_surf_results.m
M       cat_vol_groupwise_ls.m
M       html/cat_starting.html

(1) Changed: Data format registered images for the longitudinal pipeline is now int16.
(2) Fixed: Wrong "&&" in cat_surf_results.m
(3) Fixed: Correct path for underlying surface if analysis was made with different SPM installation.

------------------------------------------------------------------------
r1110 | gaser | 2017-01-30 16:54:22 +0100 (Mon, 30 Jan 2017) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_stat_check_cov.m
M       cat_surf_createCS.m
M       html/cat.html

(1) Added: Surface smoothing w.r.t. local convexity to remove local artifacts.
(2) Changed: Changed selection of optional xml-files in cat_stat_check_cov.m.

------------------------------------------------------------------------
r1109 | gaser | 2017-01-26 14:53:13 +0100 (Thu, 26 Jan 2017) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       html/cat.html
M       templates_1.50mm/Template_0_IXI555_MNI152_GS.nii
M       templates_1.50mm/Template_1_IXI555_MNI152_GS.nii
M       templates_1.50mm/Template_2_IXI555_MNI152_GS.nii
M       templates_1.50mm/Template_3_IXI555_MNI152_GS.nii
M       templates_1.50mm/Template_4_IXI555_MNI152_GS.nii

Changed: Converted geodesic shooting templates to uint16.

------------------------------------------------------------------------
r1108 | gaser | 2017-01-26 14:09:32 +0100 (Thu, 26 Jan 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m

Fixed: Missing parameter in cat_main.m for LAS=0 and native segmentation.

------------------------------------------------------------------------
r1107 | gaser | 2017-01-25 14:00:10 +0100 (Wed, 25 Jan 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_tst_qa.m

Changed: Supress opengl warning in cat_tst_qa.m in batch mode.

------------------------------------------------------------------------
r1106 | gaser | 2017-01-24 16:22:20 +0100 (Tue, 24 Jan 2017) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_plot_boxplot.m
 M      html/cat_methods_validation.html
 M      html/images/cat_tst_seg_BWP_boxplot.png
 M      html/images/cat_tst_seg_BWP_detail.png
 M      html/images/cat_tst_seg_real_boxplot.png
 M      html/images/cat_tst_seg_real_detail.png

Fixed: cat_plot_boxplot.m did not worked correctly if no additional flags were
defined.


------------------------------------------------------------------------
r1105 | gaser | 2017-01-24 15:51:31 +0100 (Tue, 24 Jan 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_check_cov.m
M       html/cat_methods_validation.html

(1) Fixed: Slice for samples 2..n were not displayed in cat_stat_check_cov.m.
(2) Changed: Updated HTML documentation about segmentation validation.

------------------------------------------------------------------------
r1104 | dahnke | 2017-01-24 15:05:43 +0100 (Tue, 24 Jan 2017) | 34 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main.m
M       cat_main_registration.m
M       cat_plot_boxplot.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job_APP_init.m
M       cat_tst_calc_kappa.m
M       cat_tst_cattest.m
M       html/cat.html
M       html/cat_methods.html
A       html/cat_methods_validation.html
A       html/images/cat_tst_seg_BWP_boxplot.png
A       html/images/cat_tst_seg_BWP_detail.png
A       html/images/cat_tst_seg_real_boxplot.png
A       html/images/cat_tst_seg_real_detail.png
 M      internal

(1)  Fixed:   Corrected APP GUI type from natural (1..n) to whole (0..n) number.
(2)  New:     Added "validation" HTML page with BWP and expert segmentation
              results of SPM, VBM, and CAT releases.
(3)  Fixed:   Updated lazy preprocessing
(4)  Changed: Updated axis limitation in "cat_plot_boxplot" to avoid ignoring
              of outliers. Further changes to control yticks and ylabels.
(5)  Changed: Updated lazy processing (developer mode), to rerun batches and
              avoid reprocessing of successful processed images in case of
              "segmentation violation" errors that killed previous Matlab
              instances.
(6) Fixed:    Corrected division by zero warnings in "cat_run_job_APP_init".
(7) Changed:  Updated color range in "cat_tst_calc_kappa" in case of real data.
(8) Changed:  Added "extops.regstr" parameter in "cat_tst_cattest".

------------------------------------------------------------------------
r1103 | gaser | 2017-01-13 11:01:32 +0100 (Fri, 13 Jan 2017) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_io_FreeSurfer.m
M       cat_main_gintnorm.m
M       cat_main_registration.m
M       cat_run_job.m
M       cat_vol_iscale.m
M       cat_vol_partvol.m

Changed: Typos...

------------------------------------------------------------------------
r1102 | gaser | 2017-01-13 10:04:42 +0100 (Fri, 13 Jan 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_analyze_ROIs.m

Changed: In cat_stat_analyze_ROIs.m there is now an option to manually select
missing label files if the files were moved. Furthermore, some measures such
as thickness of voxel analysis are now deselected.

------------------------------------------------------------------------
r1101 | dahnke | 2017-01-11 16:23:32 +0100 (Wed, 11 Jan 2017) | 50 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_io_FreeSurfer.m
M       cat_io_report.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_main_LASs.m
M       cat_main_gintnorm.m
M       cat_main_gintnormi.m
M       cat_main_registration.m
M       cat_run_job.m
M       cat_run_job_APP_final.m
M       cat_run_job_APP_init.m
M       cat_tst_qa.m
M       cat_vol_div.m
M       cat_vol_grad.m
M       compile.m
M       ds.m

(1)  Fixed*:  Invert Jacobian determinant in Shooting.
(2)  Fixed*:  Corrected problems in "cat_run_APP_init", ("cat_run_APP_final",)
              "cat_main", "cat_main_gintnorm", "cat_main_LAS", "cat_main_LASs",
              and "cat_io_report" for negative T1 values (BWP MS images).
(3)  Fixed*:  Corrected problems in "cat_run_APP_init", ("cat_run_APP_final",)
              "cat_main", "cat_main_gintnorm", "cat_main_LAS", "cat_main_LASs",
              and "cat_io_report" for images with backgrounds with intensities
              like the object, e.g., BG=0.8, CSF=0.0, GM=0.5, WM=1.0.
(4)  Fixed:   Corrected rng error of old MATLAB versions in "compile".
(5)  Fixed:   NaN-uint8 error in "cat_run_job".
(6)  Fixed:   Corrected reduction condition for cat_main_gintnorm in "cat_main".
(7)  Fixed:   Improved behaviour for NaN background values in APP.
(8)  Fixed:   Corrected thresholds in "cat_main_registration".
(9)  Fixed:   Corrected creation of SPM-Segmentation error in "cat_main".
(10) Fixed:   Corrected creation of low-tissue-contrast warning in
              "cat_main_gintnorm".
(11) Fixed:   Corrected missing field in "cat_surf-surf2roi".
(12) New:     Added switch to APP4/5 processing in case of failed affine
              registration. Switch to APP0 processing in case of failed initial
              APP processing.
(13) Changed: Updated "cat.extopts.regstr" with eps (fast) - 1 (accurate) for
              optimized Shooting with default=0.5 that takes about ~200 seconds
              (similar to Dartel).
(14) Fixed:   Added file type check for read functions in "cat_io_FreeSurfer" to
              avoid reading of gifti, nifti, and Matlab files.
(15) Fixed:   Added NaN-replacement by nearest non NaN value in "cat_vol_grad"
              and "cat_vol_div".


------------------------------------------------------------------------
r1100 | gaser | 2017-01-10 16:24:06 +0100 (Tue, 10 Jan 2017) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_surf2roi.m
 M      templates_1.50mm/Template_0_IXI555_MNI152_GS.nii
 M      templates_1.50mm/Template_1_IXI555_MNI152_GS.nii
 M      templates_1.50mm/Template_2_IXI555_MNI152_GS.nii
 M      templates_1.50mm/Template_3_IXI555_MNI152_GS.nii
 M      templates_1.50mm/Template_4_IXI555_MNI152_GS.nii

Fixed: Surface ROI values for the right hemisphere in cat_surf_surf2ROIs.m
were not correct. Thanks to Ren� Seiger for pointing to that issue.


------------------------------------------------------------------------
r1099 | gaser | 2016-12-30 11:40:38 +0100 (Fri, 30 Dec 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_calc.m
M       cat_surf_vol2surf.m

(1) Changed: Mapped surfaces in template space now always have .gii extension.
(2) Fixed: Check for doubled .gii extension in output name for calculating
    surfaces in cat_surf_calc.m.

------------------------------------------------------------------------
r1098 | gaser | 2016-12-28 12:04:30 +0100 (Wed, 28 Dec 2016) | 15 lines

Changed paths:
M       CHANGES.txt
A       templates_1.50mm/Template_0_IXI555_MNI152_GS.nii
D       templates_1.50mm/Template_0_NKI174_MNI152_GS.nii
A       templates_1.50mm/Template_1_IXI555_MNI152_GS.nii
D       templates_1.50mm/Template_1_NKI174_MNI152_GS.nii
A       templates_1.50mm/Template_2_IXI555_MNI152_GS.nii
D       templates_1.50mm/Template_2_NKI174_MNI152_GS.nii
A       templates_1.50mm/Template_3_IXI555_MNI152_GS.nii
D       templates_1.50mm/Template_3_NKI174_MNI152_GS.nii
A       templates_1.50mm/Template_4_IXI555_MNI152_GS.nii
D       templates_1.50mm/Template_4_NKI174_MNI152_GS.nii

Changed: Updated Geodesic Shooting templates using IXI database.

------------------------------------------------------------------------
r1097 | gaser | 2016-12-21 13:39:22 +0100 (Wed, 21 Dec 2016) | 10 lines

Changed paths:
M       CHANGES.txt
MM      cat_main_registration.m
M       cat_surf_vol2surf.m

(1) Changed: Changed output names of volume-to-surface mapping.
(2) Changed: Changed minimum file number for covariance check to allow selection
    of 4D data.


------------------------------------------------------------------------
r1096 | gaser | 2016-12-21 13:19:36 +0100 (Wed, 21 Dec 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_surf_vol2surf.m

(1) Changed: Changed output names of volume-to-surface mapping.
(2) Changed: Changed minimum file number for covariance check to allow selection
    of 4D data.


------------------------------------------------------------------------
r1095 | dahnke | 2016-12-19 12:13:35 +0100 (Mon, 19 Dec 2016) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_io_report.m
M       cat_main.m
A       cat_main_registration.m
M       cat_run_job.m
M       cat_vol_isarnlm.m

(1) Fixed:    Further corrections in "cat_io_report".
(2) Changed:  Added subject number in preprocessing command line report.
(3) Added:    cat_main_registration.
(4) Changed:  Corrected command line output of "cat_vol_isarnlm" that also
              include changes in "cat_main" and "cat_run_job".
(5) Changed:  Reformat AMAP parameter and refined error detection based AMAP
              output.

------------------------------------------------------------------------
r1094 | gaser | 2016-12-19 11:45:37 +0100 (Mon, 19 Dec 2016) | 12 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       cat_defaults.m
M       html/cat.html

Fixed: Corrected some typos.


------------------------------------------------------------------------
r1093 | dahnke | 2016-12-15 15:37:27 +0100 (Thu, 15 Dec 2016) | 53 lines

Changed paths:
M       CHANGES.txt
M       batches/cattest/cat12_202_VBM_tools.m
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_io_FreeSurfer.m
M       cat_io_report.m
M       cat_io_writenii.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_main_LASs.m
M       cat_main_cleanup.m
M       cat_main_gcut.m
M       cat_main_gintnorm.m
M       cat_parallelize.m
M       cat_run_job_APP_final.m
M       cat_run_newcatch.m
M       cat_run_oldcatch.m
M       cat_surf_calc.m
M       cat_surf_parameters.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
M       cat_surf_smooth.m
M       cat_surf_surf2roi.m
M       cat_tst_cattest.m
M       cat_tst_qa.m
M       cat_vol_grad.m
M       cat_vol_partvol.m
M       cat_vol_pbt.m
M       compile.m
M       internal/cat_io_volctype.m
M       tbx_cfg_cat.m
M       templates_1.50mm/Template_0_NKI174_MNI152_GS.nii
M       templates_1.50mm/Template_1_NKI174_MNI152_GS.nii
M       templates_1.50mm/Template_2_NKI174_MNI152_GS.nii
M       templates_1.50mm/Template_3_NKI174_MNI152_GS.nii
M       templates_1.50mm/Template_4_NKI174_MNI152_GS.nii

(1) Fixed:    Updated Shooting template.
(2) Fixed:    Removed "extopts.debug".
(3) Changed:  Added "extopts.scale_cortex" and "extopts.add_parahipp" to
              expert and developer GUI.
(4) Changed:  Moved registration to a separate function "cat_main_registration"
              that include Dartel, default Shooting, and optimised Shooting.
              Added "cat.extopts.regstr" to "cat_defaults" and expert and
              developer GUI.
              Changed interpolation in "cat_io_writenii" to increase speed.
(5) Fixed:    Corrected round error for older Matlab versions in
              "cat_run_job_APP_final".
(6) Fixed:    Corrected output in case of gcut errors.
(7) Fixed:    Corrected output of APP and interpolation type in CAT report.
(8) Fixed:    Corrected problems in "cat_io_report".

------------------------------------------------------------------------
r1092 | gaser | 2016-11-30 13:41:11 +0100 (Wed, 30 Nov 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m

Changed: Surface deformation was optimized in cat_surf_createCS.m.


------------------------------------------------------------------------
r1091 | gaser | 2016-11-30 12:56:07 +0100 (Wed, 30 Nov 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       html/cat.html

Changed: Minimum file number for cat_stat_check_cov.mis now 3.

------------------------------------------------------------------------
r1090 | gaser | 2016-11-30 11:17:18 +0100 (Wed, 30 Nov 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m

Fixed: Forgot to remove debug flag in cat_surf_createCS.m.

------------------------------------------------------------------------
r1089 | gaser | 2016-11-30 11:01:18 +0100 (Wed, 30 Nov 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_check_cov.m
M       cat_surf_createCS.m

(1) Changed: Surface deformation was optimized in cat_surf_createCS.m.
(2) Fixed: In cat_stat_check_cov.m comparison of filenames was not correct
    if length was differing (thanks to Raphael Casseb for correcting this
    error).

------------------------------------------------------------------------
r1088 | gaser | 2016-11-25 11:33:11 +0100 (Fri, 25 Nov 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_io_writenii.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Changed: Interpolation in cat_io_writenii.m was set to previous version.
(2) Fixed: In tbx_cfg_cat.m the expert case argument was wrong.

------------------------------------------------------------------------
r1087 | gaser | 2016-11-23 13:56:20 +0100 (Wed, 23 Nov 2016) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_io_writenii.m
M       cat_run_job.m
M       cat_surf_createCS.m
M       cat_tst_cattest.m
M       cat_vol_pbt.m

(1) Changed: Removed tca and replaced this approach by a local change of
    intensities for creating the initial surface. In the parahippocampal
    area the intensity of the ppi image is inceased. This prevents large
    cuts in that area. In the cortex the ppi intensity is decreased which
    helps in preventing glued gyri/sulci.
(2) Changed: Added two new parameters to control surface creation in
    cortex and parahippocampal gyrus.
(3) Changed: Typos...

------------------------------------------------------------------------
r1086 | dahnke | 2016-11-23 11:51:01 +0100 (Wed, 23 Nov 2016) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
M       cat_run_job.m
M       tbx_cfg_cat.m

(1) Fixed:    Added missed bias variable for PDF report (experimental mode).
(2) New:      Extend surface variable to control the side reconstruction.


------------------------------------------------------------------------
r1085 | dahnke | 2016-11-23 10:24:23 +0100 (Wed, 23 Nov 2016) | 26 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_io_writenii.m
M       cat_main.m
M       cat_run_job.m
M       cat_surf_createCS.m
M       cat_tst_cattest.m

(1) Deleted:  Removed "debug" variable and added further state to "verb".
(2) Added:    Added "experimental" variable to control new functions that
              are still in development.
(3) Fixed:    Small corrections.
(4) Changed:  Updated cat PDF report:
              * removed WMH volume if WMHC<2 (no volume correction)
                but added red warning string if there are uncorrected WMHs with
                more than 3% of TIV or 5% of WM that also create the WMH warning
              * added 'e' for expert and 'd' for developer GUI to version number
              * added 'x' for experimental to version number
              * added spatial normalization resolution
              * moved APP to affine registration entry
              * moved NCstr to noise reduction entry
              * added SPM bias and sampling parameter (experimental mode only)

------------------------------------------------------------------------
r1084 | dahnke | 2016-11-22 10:33:32 +0100 (Tue, 22 Nov 2016) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_io_writenii.m
M       cat_main.m
M       cat_run_job.m
M       cat_tst_cattest.m

(1) Fixed:    Added interpolation of Yy in "cat_io_writenii" to reduce artefacts,
              if the voxel resolution of the original image is lower that of the
              template.
(2) Fixed:    Corrected "best" interpolation setting in "cat_run_job".


------------------------------------------------------------------------
r1083 | dahnke | 2016-11-21 15:11:02 +0100 (Mon, 21 Nov 2016) | 19 lines

Changed paths:
M       CHANGES.txt
M       batches/cattest/cat12_101_MAIN_segment.m
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
M       cat_run.m
M       cat_run_job_APP_final.m
M       cat_tst_cattest.m
M       cat_vol_pbtp.mexmaci64

(1) Fixed:    Corrected error in case of APP=4 / APP=5 with bad CSF threshold of
              low resolution data in "cat_run_job_APP_final".
(2) Fixed:    Corrected error in case of gcutstr=0 with bad brain mask generation
              in "cat_main".
(3) Fixed:    Corrected dim error in case of cleanupstr=0 in "cat_main".
(4) New:      Added MRF and TCA entries in developer GUI.
(5) Deleted:  Removed BB in cat_defaults because it is not required anymore.

------------------------------------------------------------------------
r1082 | gaser | 2016-11-18 15:23:06 +0100 (Fri, 18 Nov 2016) | 9 lines

Changed paths:
M       CHANGES.txt
MM      batches/cattest/cat12_201_VBM_deformation.m
MM      batches/cattest/cat12_203_VBM_exportRBM.m
MM      batches/cattest/cat12_309_SBM_exportRBM.m
M       cat12.fig

Changed: Interactive help is now called as separate window from CAT12 GUI.

------------------------------------------------------------------------
r1081 | gaser | 2016-11-18 15:07:37 +0100 (Fri, 18 Nov 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_main.m

Changed: Typos...

------------------------------------------------------------------------
r1080 | dahnke | 2016-11-18 14:45:44 +0100 (Fri, 18 Nov 2016) | 53 lines

Changed paths:
M       CHANGES.txt
A  +    batches/cattest/cat12_101_MAIN_segment.m
A  +    batches/cattest/cat12_102_MAIN_segment_greaterapes.m
A  +    batches/cattest/cat12_103_MAIN_segment_oldworldmonkeys.m
A  +    batches/cattest/cat12_104_MAIN_segment_SPM.m
A       batches/cattest/cat12_201_VBM_deformation.m
A  +    batches/cattest/cat12_202_VBM_tools.m
A       batches/cattest/cat12_203_VBM_exportRBM.m
A  +    batches/cattest/cat12_301_SBM_extractAddSurfPara.m
A  +    batches/cattest/cat12_302_SBM_MapNormVol2AvgSurf.m
A  +    batches/cattest/cat12_303_SBM_MapVol2IndSurf.m
A  +    batches/cattest/cat12_304_SBM_ResampAndSmooth.m
A  +    batches/cattest/cat12_305_SBM_SurfCalc.m
A  +    batches/cattest/cat12_308_SBM_Surf2ROI.m
A       batches/cattest/cat12_309_SBM_exportRBM.m
D       batches/cattest/cat12_SBM_101_segment.m
D       batches/cattest/cat12_SBM_102_segment_greaterapes.m
D       batches/cattest/cat12_SBM_103_segment_oldworldmonkeys.m
D       batches/cattest/cat12_SBM_201_extractAddSurfPara.m
D       batches/cattest/cat12_SBM_202_MapNormVol2AvgSurf.m
D       batches/cattest/cat12_SBM_203_MapVol2IndSurf.m
D       batches/cattest/cat12_SBM_204_ResampAndSmooth.m
D       batches/cattest/cat12_SBM_205_SurfCalc.m
D       batches/cattest/cat12_SBM_206_tools.m
D       batches/cattest/cat12_SBM_301_Surf2ROI.m
D       batches/cattest/cat12_SBM_302_exportRBM.m
D       batches/cattest/cat12_SBM_401_SBM_and_RBM_for_SPM.m
M       cat_conf_extopts.m
M       cat_io_report.m
M       cat_main.m
M       cat_main_cleanup.m
M       cat_main_gcut.m
M       cat_plot_boxplot.m
M       cat_run_job.m
M       cat_tst_cattest.m
M       compile.m

(1) Fixed*:    Corrected iy map output.
(2) Fixed*:    Corrected error "cat_main_gcut".
(3) Fixed:     Corrected small print error in "cat_io_report".
(4) Fixed:     Corrected small error for cleanupstr==0.
(5) Fixed:     Corrected handling and help text of APPfull parameter.
(6) Changed:   Updated "cat_tst_cattest", renamed test batches, and added
               "cat12_201_VBM_deformation" with test of y and iy for SPM and
               CAT deformation utilities.
(7) Changed:   Unfinal modifications of Shooting pipeline.






------------------------------------------------------------------------
r1079 | gaser | 2016-11-17 13:54:11 +0100 (Thu, 17 Nov 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m

Changed: Fine-tuned spherical registration parameters in cat_surf_createCS.m

------------------------------------------------------------------------
r1078 | gaser | 2016-11-16 21:21:31 +0100 (Wed, 16 Nov 2016) | 10 lines

Changed paths:
M       CHANGES.txt
D       cat_conf_fmri.m
M       cat_conf_stools.m
D       cat_fmri_main.m
D       cat_fmri_multi_run.m

(1) Removed: Deleted fmri function that were too complex.
(2) Changed: Set absmax as default for mapping function cat_surf_vol2surf.m

------------------------------------------------------------------------
r1077 | gaser | 2016-11-15 21:07:42 +0100 (Tue, 15 Nov 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_plot_circular.m
M       cat_stat_analyze_ROIs.m

Changed: Prepared comparison of correlation matrices in cat_stat_analyze_ROIs.m

------------------------------------------------------------------------
r1076 | gaser | 2016-11-14 13:06:04 +0100 (Mon, 14 Nov 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_results.m
M       html/cat.html

Fixed: Datatips were not reset in cat_surf_results.m

------------------------------------------------------------------------
r1075 | gaser | 2016-11-11 12:33:00 +0100 (Fri, 11 Nov 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_conf_tools.m

Changed: Restricted load of xml-files for cat_stat_checkcov.m.

------------------------------------------------------------------------
r1074 | gaser | 2016-11-11 12:21:54 +0100 (Fri, 11 Nov 2016) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_surf_createCS.m
M       html/cat.html
M       html/cat_starting.html

Changed: Updated help text and quick starting guide.

------------------------------------------------------------------------
r1073 | gaser | 2016-11-10 15:57:30 +0100 (Thu, 10 Nov 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m

Fixed: Solved error when multiple surfaces were selected for just one hemipshere
in cat_surf_results.

------------------------------------------------------------------------
r1072 | dahnke | 2016-11-09 16:01:16 +0100 (Wed, 09 Nov 2016) | 27 lines

Changed paths:
M       CHANGES.txt
M       batches/cattest/cat12_SBM_201_extractAddSurfPara.m
M       batches/cattest/cat12_SBM_302_exportRBM.m
M       cat_conf_stools.m
M       cat_io_FreeSurfer.m
M       cat_main_gcut.m
M       cat_main_gcut_DEV.m
M       cat_surf_fun.m
M       cat_surf_info.m
M       cat_surf_parameters.m
M       cat_surf_render.m
M       cat_surf_render2.m
M       cat_tst_cattest.m
M       cat_tst_qa.m

(1) Fixed:    Corrected error message handling in "cat_main_gcut" that now
              throws an error if the brain mask is empty.
(2) Fixed:    Corrected name/texture handling in "cat_surf_info".
(3) Fixed:    Small corrections in "cat_surf_render2".
(4) Fixed:    Corrected errors in "gii2fs" in "cat_surf_FreeSurfer".
(5) New:      Prepared creation of inner and outer surface in "cat_surf_parameter"
              and "cat_conf_stools" in developer mode.
(6) New:      Added opengl info and data to CAT report in "cat_tst_qa".
(7) Fixed:    Small corrections in "cat_tst_cattest" and its batches.


------------------------------------------------------------------------
r1071 | gaser | 2016-11-09 14:07:47 +0100 (Wed, 09 Nov 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_spm2x.m
M       cat_surf_epivolsurf.m
M       html/cat.html

Fixed: Solved error with surfaces caused by last change in cat_stat_spm2x.m

------------------------------------------------------------------------
r1070 | dahnke | 2016-11-08 15:41:09 +0100 (Tue, 08 Nov 2016) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_epivolsurf.m
M       cat_surf_fun.m
M       cat_surf_gyrification.m
M       ds.m

(1) Fixed:    Corrected smoothing problem in Laplacian GI estimation in
              "cat_surf_gyrification" and "cat_surf_epivolsurf".
(2) Fixed:    Corrected error in hull estimation in "cat_surf_fun".
(3) Changed:  Added surface render to "ds".



------------------------------------------------------------------------
r1069 | gaser | 2016-11-08 15:27:45 +0100 (Tue, 08 Nov 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_spm2x.m

Changed: Conversion of TFCE log-p maps is now supported in cat_stat_spm2x.m if
no conversion is selected.

------------------------------------------------------------------------
r1068 | gaser | 2016-11-08 12:42:44 +0100 (Tue, 08 Nov 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_surf_results.m
M       cat_vol_slice_overlay.m

Changed: Fonts should be now hopefully printed correctly while saving images
in cat_surf_results.m and cat_vol_slice_overlay.m.

------------------------------------------------------------------------
r1067 | dahnke | 2016-11-07 15:11:07 +0100 (Mon, 07 Nov 2016) | 22 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_main.m
M       cat_surf_createCS.m
M       cat_surf_gyrification.m
M       cat_tst_cattest.m
M       html/cat_FAQ.html
M       internal/cat_io_volctype.m
M       tbx_cfg_cat.m
M       templates_1.50mm/aal.nii
M       templates_1.50mm/cat.nii
M       templates_1.50mm/cobra.nii
D       templates_1.50mm/l1A.nii
M       templates_1.50mm/lpba40.nii

(1) Fixed:    Updated cobra atlas to HR version.
(2) Fixed:    Set aal, lpba40 and cat atlas map to uint8.
(3) Changed:  Use atlas text file for GUI help of each atlas.
(4) Fixed:    Small corrections in developer WM depth maps in "cat_surf_createCS".


------------------------------------------------------------------------
r1066 | gaser | 2016-11-07 09:21:32 +0100 (Mon, 07 Nov 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m

(1) Changed: some cosmetic changes to cat_surf_result.m


------------------------------------------------------------------------
r1065 | gaser | 2016-11-05 17:22:25 +0100 (Sat, 05 Nov 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m

(1) Changed: Added new plot to cat_surf_results and changed positions and
    saving.
(2) Changed: Added use of "y" as global variable in cat12.m for calling
    cat_surf_results.m

------------------------------------------------------------------------
r1064 | gaser | 2016-11-04 13:15:13 +0100 (Fri, 04 Nov 2016) | 14 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_main_gcut.m
M       cat_main_gcut_DEV.m
M       cat_surf_createCS.m
M       html/cat.html

(1) Changed: Added information that ROI estimates are in native space to manual.
(2) Changed: Replaced "Ventricle closing" by "Ventricle filling"
(3) Changed: Changed paramter for tca back to 10000 for largest component.

------------------------------------------------------------------------
r1063 | dahnke | 2016-11-02 17:56:10 +0100 (Wed, 02 Nov 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m

(1)  Fixed:   Corrected small errors in ROI atlas selection.


------------------------------------------------------------------------
r1062 | dahnke | 2016-11-02 16:37:53 +0100 (Wed, 02 Nov 2016) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_main.m
M       cat_run.m
M       cat_run_job.m
M       tbx_cfg_cat.m

(1)  Changed:  Updated ROI atlas processing for high resolution atlas maps.
(2)  Changed:  Added atlas selection to expert/developer GUI

------------------------------------------------------------------------
r1061 | dahnke | 2016-11-01 14:57:22 +0100 (Tue, 01 Nov 2016) | 24 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_LASs.m
M       cat_run_job.m
M       cat_surf_createCS.m
M       cat_surf_info.m
M       cat_surf_render2.m

(1)  Fixed:    Corrected problems in 'Synchronise Views' with special angles and
               zoom levels in "cat_surf_render2".
(2)  Fixed:    Corrected parameter setting in "cat_surf_createCS" and restricted
               blood vessel correction to CAT preprocessing.
(3)  Fixed:    Corrected error in biasreg estimation in "cat_run_job".
(4)  Changed:  Increased basic AMAP sub parameter from 16 to 32 to obtain more
               stable results in fine brain regions, e.g., occipital lobe, that
               showed WM overestimation before.
(5)  Changed:  Tested surface reconstruction of the cerebellum and added "ch"
               side identifier to "cat_surf_info" and "cat_surf_render2".
(6)  Changed:  Small corrections in "cat_main_LASs".
(7)  Changed:  Updated distance estimation of WM and CSF in "cat_surf_createCS
               from "cat_vbdist" to cat_vol_eidist".


------------------------------------------------------------------------
r1060 | gaser | 2016-10-29 12:02:45 +0200 (Sat, 29 Oct 2016) | 7 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt

Changed: Updated CAT12 manual

------------------------------------------------------------------------
r1059 | gaser | 2016-10-28 00:39:05 +0200 (Fri, 28 Oct 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       html/cat.html
M       html/cat.txt

Changed: Updated html code and corrected typos and language issues.

------------------------------------------------------------------------
r1058 | gaser | 2016-10-28 00:15:12 +0200 (Fri, 28 Oct 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       html/cat.html

Changed: Updated html code and corrected typos and language issues.

------------------------------------------------------------------------
r1057 | gaser | 2016-10-28 00:08:23 +0200 (Fri, 28 Oct 2016) | 19 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       html/cat.html
M       html/cat_methods_FN.html
M       html/cat_methods_QA.html
M       html/cat_methods_RBM.html
M       html/cat_methods_VBM.html
M       html/cat_methods_VBM_APP.html
M       html/cat_methods_defaults.html
M       html/cat_methods_errormanagement.html
M       html/cat_tools.html
M       html/cat_tools_ROI.html
M       html/cat_tools_SBM.html
M       html/cat_tools_VBM.html
MM      internal/cat_vol_flipside.m

Changed: Updated html code and corrected typos and language issues.

------------------------------------------------------------------------
r1056 | gaser | 2016-10-27 21:49:48 +0200 (Thu, 27 Oct 2016) | 9 lines

Changed paths:
M       CHANGES.txt

(1) Fixed: Changed interpolation for applying deformations in long. batch to
    trilinear interpolation because b-spline interpolation resulted in neg.
    values for writing GM/WM maps.
(2) Changed: ROI option is now also available in standard mode because of
    interferences with long. batch mode.

------------------------------------------------------------------------
r1055 | gaser | 2016-10-27 21:49:16 +0200 (Thu, 27 Oct 2016) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_long_main.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Fixed: Changed interpolation for applying deformations in long. batch to
    trilinear interpolation because b-spline interpolation resulted in neg.
    values for writing GM/WM maps.
(2) Changed: ROI option is now also available in standard mode because of
    interferences with long. batch mode.

------------------------------------------------------------------------
r1054 | dahnke | 2016-10-27 12:10:46 +0200 (Thu, 27 Oct 2016) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_render2.m
A       internal/cat_vol_flipside.m

(1)  Fixed:   Corrected setting of PBT resolution between 0.10 and 1.00 mm.
(2)  New:     Added internal function to manually flip the side of images.
(3)  New:     Renamed "cat_surf_render2" GUI functions 'Synchronise Views' to
              'Synchronise Views Once' and added 'Synchronise Views' that
              synchronise views as long as the field is active.
              Added 'Thickness' as intensity range between 0 and 6.

------------------------------------------------------------------------
r1053 | dahnke | 2016-10-26 17:44:10 +0200 (Wed, 26 Oct 2016) | 16 lines

Changed paths:
M       CHANGES.txt
MM      batches/cat12batch_RBM_and_SBM_for_SPM.m
MM      batches/cattest/cat12_SBM_205_SurfCalc.m
MM      batches/cattest/cat12_SBM_206_tools.m
MM      batches/cattest/cat12_SBM_401_SBM_and_RBM_for_SPM.m
M       cat_conf_stools.m
M       cat_main.m
M       cat_main_LASs.m
M       cat_tst_cattest.m

(1)  Fixed:   Corrected error in "cat_conf_stools".
(2)  Fixed:   Corrected small test error in "cat_tst_testcat".
(3)  Fixed:   Corrected background problems in "cat_main_LASs" that lead to
              thickness overestimation in BUSS.

------------------------------------------------------------------------
r1052 | dahnke | 2016-10-26 16:01:23 +0200 (Wed, 26 Oct 2016) | 44 lines

Changed paths:
 M      .
M       CHANGES.txt
 M      batches
A       batches/cat12batch_RBM_and_SBM_for_SPM.m
A       batches/cattest/cat12_SBM_205_SurfCalc.m
A       batches/cattest/cat12_SBM_206_tools.m
M       batches/cattest/cat12_SBM_301_Surf2ROI.m
A       batches/cattest/cat12_SBM_401_SBM_and_RBM_for_SPM.m
M       cat_conf_tools.m
M       cat_io_cprintf.m
M       cat_main.m
M       cat_main_LASs.m
M       cat_run_job.m
M       cat_stat_showslice_all.m
M       cat_surf_info.m
M       cat_tst_cattest.m
M       compile.m
 M      data
M       html/cat_FAQ.html
M       html/images/CAT_PBT_for_SPM.png
 M      internal
M       spm_cat12.m
M       tbx_cfg_cat.m
 M      templates_animals
 M      templates_surfaces

(1)  Fixed:   Corrected batch mode error in sanlm output.
              Added NCstr in GUI input.
(2)  Fixed:   Corrected input handling in SPM RBM and SBM preprocessing
              pipeline of "cat_main" and "cat_run_job".
(3)  Fixed:   Corrected subject name error in "cat_surf_info".
(4)  Changed: Added resolution reduction for "cat_main_LASs" to save time and
              memory. Test was ok, but MUC still have blurred sulci, 7T is ok,
              BUSS have very large thickness.
(5)  New:     Added further cattest scripts "cat12_SBM_205_SurfCalc",
              "cat12_SBM_206_tools", and "cat12_SBM_401_SBM_and_RBM_for_SPM".
(6)  New:     Added table of content in "cat_FAQ.html".
(7)  New:     Added "cat12batch_RBM_and_SBM_for_SPM" batch with sanlm denoising,
              SPM segment and CAT SPM segment.
(8)  New:     Added silent reset in "cat_io_cprintf" to reset color output.
(9)  Changed: Cleared further unused variables in "cat_main".
(10) Fixed:   Corrected error in "cat_stat_showslice_all" in case of one image.

------------------------------------------------------------------------
r1051 | gaser | 2016-10-26 11:01:27 +0200 (Wed, 26 Oct 2016) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.fig
M       cat_conf_tools.m
M       cat_stat_spm2x.m
M       cat_surf_results.m
M       html/cat.html

Changed: Updated use of atlas labeling in cat_stat_spm2x.m and now
differentiates between conversion of images and surfaces in cat12.m

------------------------------------------------------------------------
r1050 | gaser | 2016-10-26 01:16:31 +0200 (Wed, 26 Oct 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_spm2x.m

Changed: Added atlas output to cat_stat_spm2x.m

------------------------------------------------------------------------
r1049 | gaser | 2016-10-25 20:41:32 +0200 (Tue, 25 Oct 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_long_main.m
MM      cat_stat_spm2x.m

Changed: Added Dartel export for each time point to longitudinal mode.

------------------------------------------------------------------------
r1048 | gaser | 2016-10-25 18:01:41 +0200 (Tue, 25 Oct 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_spm2x.m

Changed: Conversion from spmT/F maps is now done using cat_stat_spm2x.m

------------------------------------------------------------------------
r1047 | gaser | 2016-10-25 17:53:58 +0200 (Tue, 25 Oct 2016) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_tools.m
A       cat_stat_spm2x.m
D       cat_stat_spmF2x.m
D       cat_stat_spmT2x.m
M       html/cat.html
 M      html/images/CAT_PBT_for_SPM.png

Changed: Conversion from spmT/F maps is now done using cat_stat_spm2x.m

------------------------------------------------------------------------
r1046 | gaser | 2016-10-25 11:39:25 +0200 (Tue, 25 Oct 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_vol_groupwise_ls.m
M       html/cat.html

Fixed: cat_vol_groupwise_ls.m was not working with the updated version.

------------------------------------------------------------------------
r1045 | gaser | 2016-10-24 15:22:21 +0200 (Mon, 24 Oct 2016) | 27 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat12.m
M       cat_conf_tools.m
M       cat_long_main.m
M       cat_main_LASs.m
M       cat_roi_fun.m
M       cat_stat_analyze_ROIs.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
M       html/cat.html
A       html/images/CAT_PBT_for_SPM.png
D       spm_spm_changed.m
M       tbx_cfg_cat.m

(1) Fixed: Added function to read old xml-files for mean ROI estimation.
(2) Fixed: Incorrected tag for estwrite_spm.
(3) Fixed: Added SurfaceID metadata entry for resampled data to be compatible
    to new SPM12 update.
(4) Changed: Deselected ROI estimation for long. mode for inital segmentation
    of average image.
(5) Changed: Commented out usefolder tag for ROI estimation and changed
    name for decimal_point according to its tag name.
(6) Removed: spm_spm_changed.m that is not necessary anymore.

------------------------------------------------------------------------
r1044 | gaser | 2016-10-24 00:20:37 +0200 (Mon, 24 Oct 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       spm_spm_changed.m

Changed: Now, rather use average of all surfaces in the design as default
surface for display.

------------------------------------------------------------------------
r1043 | gaser | 2016-10-23 23:38:27 +0200 (Sun, 23 Oct 2016) | 20 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cat12.m
M       cat_fmri_multi_run.m
M       cat_stat_check_cov.m
M       cat_surf_vol2surf.m
M       cat_vol_groupwise_ls.m
M       html/cat_FAQ.html
A       spm_spm_changed.m
M       tbx_cfg_cat.m

(1) Fixed: Wrong cell structure in cat_stat_check_cov.m
(2) Fixed: Typos in help textes (@Robert).
(3) Changed: Updared cat_vol_groupwise_ls.m according to new SPM12 update.
(4) Changed: In cat_surf_vol2surf.m it is now possible to only define 1 surface
    but multiple volumes. Furthermore, output name is now changed.
(5) Fixed: New SPM12 update requires SurfaceID as metadata in gifti files
    which is not gifti conform.

------------------------------------------------------------------------
r1042 | dahnke | 2016-10-22 16:28:11 +0200 (Sat, 22 Oct 2016) | 20 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_main.m
M       cat_run_job.m
M       cat_surf_createCS.m
 M      data/uint8_lowresR2x2x1_human_tumor_tp01.nii
 M      data/uint8_lowresR2x2x2_primate_chimpanzee_laz.nii
 M      data/uint8_lowresR2x2x2_primate_gibbon_gibbon4.nii
M       html/cat_FAQ.html
M       html/images/Problems_in_7_Tesla.png
M       tbx_cfg_cat.m

(1) Fixed:    Use SPM parameter update only in developer mode.
(2) Added:    Prepared CAT preprocessing of SPM segmentation in expert mode that
              required the *.nii as input data and the already processed
              c[1-3]* tissue segments and the *_seg8.mat. Added FAQ entry
              with figure with the result of both pipelines.
(3) Fixed:    Added color bars in 7 Tesla figure.

------------------------------------------------------------------------
r1041 | dahnke | 2016-10-21 09:30:41 +0200 (Fri, 21 Oct 2016) | 26 lines

Changed paths:
 M      .
M       CHANGES.txt
M       cat_main_LASs.m
M       cat_run_job.m
M       cat_run_job_APP_init.m
M       cat_tst_cattest.m
M       cat_vol_localstat.c
M       cat_vol_localstat.mexmaci64
M       compile.m
A       data
A       data/uint8_lowresR2x2x1_human_tumor_tp01.nii
A       data/uint8_lowresR2x2x2_primate_chimpanzee_laz.nii
A       data/uint8_lowresR2x2x2_primate_gibbon_gibbon4.nii

(1) Fixed:    Corrected random generator setting in "compile".
(2) Changed:  Added second output variable "mean" in case of "std" in
              "cat_vol_localstat" (required in LASs).
(3) Changed:  Reduced data setting in cat_tst_cattest.
(4) Changed:  Added bias depending SPM parameter update in "cat_run_job" and
              "cat_run_job_APP_init".
(5) Changed:  Updated and tested LASs routine that work better but still have
              smaller problems in the subcortical structures and a little bit
              to strong reconstruction by the divergence especial in biased 7T
              data with "uncorrected meninges".

------------------------------------------------------------------------
r1040 | gaser | 2016-10-20 16:33:54 +0200 (Thu, 20 Oct 2016) | 18 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_long_main.m
M       cat_run.m
M       cat_stat_check_cov.m
M       cat_surf_createCS.m
M       cat_surf_results.m
M       html/cat.html

(1) Fixed: Dependencies in cat_run.m were incorrect and ignored multiple
    files.
(2) Changed: Removed unnecessary options in cat_long_main.m.
(3) Changed: Extended cat_stat_check_conv.m for 4D data.
(4) Fixed: Threshold function in cat_surf_results was not working with
    multiple files per hemisphere.


------------------------------------------------------------------------
r1039 | gaser | 2016-10-19 15:36:46 +0200 (Wed, 19 Oct 2016) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_check_cov.m
M       cat_surf_info.m
M       cat_surf_results.m
M       html/cat.html

(1) Fixed: Added again missing initlialization of sinfo.texture in
    cat_surf_info.m
(2) Changed: Replaced spm_mesh_render by cat_surf_render in
    cat_stat_check_cov.m


------------------------------------------------------------------------
r1038 | gaser | 2016-10-19 11:51:05 +0200 (Wed, 19 Oct 2016) | 21 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main_LAS.m
MM      cat_main_LASs.m
M       cat_run.m
M       cat_surf_createCS.m
M       cat_surf_display.m
M       cat_vol_eidist.c
M       cat_vol_pbt.m
M       cat_vol_pbtp.cpp
M       compile.m
M       html/cat.html

(1) Fixed: Dependencies in cat_run.m were not all defined as cell.
(2) Fixed: Corrected many typos in help text.
(3) Fixed: Commented out use of h.sinfo in cat_surf_display that only worked
    in expert mode.
(4) Fixed: Commented out cat_check_system_output for TCA in cat_surf_createCS
    because TCA has some memory issues for very small defect sizes.

------------------------------------------------------------------------
r1037 | gaser | 2016-10-18 16:47:52 +0200 (Tue, 18 Oct 2016) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_run.m
 M      compile_standalone.txt
M       html/cat.html
M       tbx_cfg_cat.m

Fixed: Updated dependencies.

------------------------------------------------------------------------
r1036 | dahnke | 2016-10-18 16:26:32 +0200 (Tue, 18 Oct 2016) | 110 lines

Changed paths:
 M      .
M       CHANGES.txt
M       batches/cattest/cat12_SBM_102_segment_greaterapes.m
M       batches/cattest/cat12_SBM_103_segment_oldworldmonkeys.m
M       cat_amap.mexa64
M       cat_amap.mexmaci64
M       cat_amap.mexw32
M       cat_amap.mexw64
M       cat_main.m
M       cat_main_LAS.m
A       cat_main_LASs.m
M       cat_ornlm.mexa64
M       cat_ornlm.mexmaci64
M       cat_ornlm.mexw32
M       cat_ornlm.mexw64
M       cat_sanlm.mexa64
M       cat_sanlm.mexmaci64
M       cat_sanlm.mexw32
M       cat_sanlm.mexw64
M       cat_stat_nanmean.m
M       cat_stat_nanmedian.m
M       cat_stat_nanstat1d.m
M       cat_stat_nanstd.m
M       cat_stat_nansum.m
M       cat_surf_createCS.m
M       cat_surf_display.m
M       cat_surf_info.m
M       cat_surf_render2.m
M       cat_tst_cattest.m
M       cat_vbdist.c
M       cat_vbdist.mexa64
M       cat_vbdist.mexmaci64
M       cat_vbdist.mexw64
M       cat_vol_downcut.mexa64
M       cat_vol_downcut.mexmaci64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.c
M       cat_vol_eidist.mexa64
M       cat_vol_eidist.mexmaci64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.mexa64
M       cat_vol_genus0.mexmaci64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mexa64
M       cat_vol_gradient3.mexmaci64
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mexa64
M       cat_vol_interp3f.mexmaci64
M       cat_vol_interp3f.mexw64
M       cat_vol_isarnlm.m
M       cat_vol_laplace3.mexa64
M       cat_vol_laplace3.mexmaci64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mexa64
M       cat_vol_laplace3R.mexmaci64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexa64
M       cat_vol_localstat.mexmaci64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexa64
M       cat_vol_median3.mexmaci64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexa64
M       cat_vol_median3c.mexmaci64
M       cat_vol_median3c.mexw64
M       cat_vol_pbt.m
M       cat_vol_pbtp.cpp
M       cat_vol_pbtp.mexa64
M       cat_vol_pbtp.mexmaci64
M       cat_vol_pbtp.mexw64
A  +    cat_vol_reduceRes.m
M       cat_vol_sanlm.m
M       cat_vol_simgrow.mexa64
M       cat_vol_simgrow.mexmaci64
M       cat_vol_simgrow.mexw64
D       cattest
M       compile.m
M       development/cat_main_LAS.m
M       development/cat_surf_createCS.m
M       internal/cat_vol_cMRegularizarNLM3D.mexmaci64
D       internal/cat_vol_reduceRes.m
M       spm_cat12.m
 M      templates_1.50mm
A  +    templates_animals/ape_greater_cat.nii
D       templates_animals/ape_greater_vbm12.nii
A  +    templates_animals/monkey_oldworld_cat.nii
D       templates_animals/monkey_oldworld_vbm12.nii

(1) Fixed:    "cat_main" updates:
              - Corrected error in case of LAS=0
              - Increased masking for surface creation
              - Limited resolution of global intensity normalization
(2) Changed:  Renamed animal atlas map "vbm12" to "cat".
(3) Fixed:    Refined name field in "cat_surf_info".
(4) Fixed:    "cat_surf_render2" upates:
              - Corrected display of defect maps
              - Corrected colorbar handling in save image function
              - Added texture transparency to "cat_surf_render2"
(5) Changed:  Updated "compile" function by further tests.
(6) Changed:  Moved "cat_vol_reduceRes" from internal to cat main directory.
(7) Changed:  Memory optimization of "cat_vol_sanlm" and "cat_vol_isarnlm".
(8) Fixed:    Corrected single data type error in "cat_stat_nanmean",
              "cat_stat_nansum", and "cat_stat_nanstd" and "cat_stat_nanstat1d"
              for large arrays. Added help and test case.
(9) Added:    Prepared "cat_main_LASs" an improved version of "cat_main_LAS".




------------------------------------------------------------------------
r1035 | gaser | 2016-10-17 17:13:07 +0200 (Mon, 17 Oct 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m

Fixed: Always use "gifti" as filter for surface data in cat_conf_stools.m.

------------------------------------------------------------------------
r1034 | gaser | 2016-10-17 11:37:32 +0200 (Mon, 17 Oct 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_surf_vol2surf.m
A       compile_standalone.txt
M       html/cat.html

Fixed: Always use "gifti" as filter for surface data in cat_conf_stools.m.

------------------------------------------------------------------------
r1033 | gaser | 2016-10-14 23:23:17 +0200 (Fri, 14 Oct 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m
 M      cat_vol_iscaling.m
 M      html/images/Gyral_blurring.png
 M      html/images/Problems_in_7_Tesla.png
 M      html/images/Sulcal_blurring.png

Changed: Added option to rotate views in cat_surf_results.m.

------------------------------------------------------------------------
r1032 | gaser | 2016-10-14 01:54:19 +0200 (Fri, 14 Oct 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_results.m

Changed: Added optional bottom view to cat_surf_results.m.

------------------------------------------------------------------------
r1031 | gaser | 2016-10-11 10:39:54 +0200 (Tue, 11 Oct 2016) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_surf_results.m
M       html/cat.html
M       html/cat_FAQ.html

(1) Changed: Some changes to cat_surf_results to better deal with thresholds.
(2) Fixed: estroi was not defined in expert mode in cat_conf_stools.m and is
    currently commented out and not used.

------------------------------------------------------------------------
r1030 | dahnke | 2016-10-05 17:37:43 +0200 (Wed, 05 Oct 2016) | 7 lines

Changed paths:
M       CHANGES.txt
A       cat_vol_iscaling.m

(1) New:   Addend forgotten "cat_vol_iscaling".


------------------------------------------------------------------------
r1029 | dahnke | 2016-10-05 16:57:30 +0200 (Wed, 05 Oct 2016) | 23 lines

Changed paths:
M       CHANGES.txt
M       cat_main_LAS.m
M       cat_surf_createCS.m
M       cat_tst_cattest.m
M       development/cat_main_LAS.m
M       development/cat_surf_createCS.m
M       html/cat_FAQ.html
A       html/images/Gyral_blurring.png
A       html/images/Problems_in_7_Tesla.png
A       html/images/Sulcal_blurring.png
 M      internal
 M      templates_1.50mm
M       templates_1.50mm/cat.nii
 M      templates_animals

(1) Changed:  Refined human CAT atlas.
(2) Changed:  Corrections in "cat_main_LAS" to avoid gyral blurring.
(3) Changed:  Added further WMH correction in "cat_surf_createCS".
(4) Changed:  Added 3 comments in "cat_FAQ.html" for blurred sulci/gyri and
              unsolved problems in 7 Tesla images with strong inhomogeneities.


------------------------------------------------------------------------
r1028 | gaser | 2016-10-05 15:06:52 +0200 (Wed, 05 Oct 2016) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_main.m
D       cat_stat_ROI.m
M       cat_stat_analyze_ROIs.m
M       cat_stat_check_cov.m
M       cat_surf_results.m
D       cat_vol_calc_roi.m

(1) Changed: Removed saving of intensity values in xml-files.
(2) Changed: Many changes to cat_surf_results to automatically get thresholds.
(3) Fixed: Updated cat_stat_check_cov to correctly use xml-content from
    cat_io_xml.m.
(4) Changed: Updated cat_stat_analyze_ROIs.m to deal with old and new xml-files.
(5) Removed: cat_stat_ROI, that is replaced by cat_roi_fun.m.
(6) Removed: cat_vol_calc_roi.m

------------------------------------------------------------------------
r1027 | gaser | 2016-10-04 21:27:07 +0200 (Tue, 04 Oct 2016) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_analyze_ROIs.m
M       cat_stat_spmT2x.m
M       cat_surf_results.m

(1) Fixed: Bug in cat_stat_spmT2x.m for images with no voxel threshold.
(2) Changed: cat_surf_results updates now colorbar according to minimal
    and maximal values <> 0 in the image.


------------------------------------------------------------------------
r1026 | gaser | 2016-10-03 22:44:40 +0200 (Mon, 03 Oct 2016) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
MM      cat_roi_fun.m
M       cat_run_job.m
M       cat_stat_IQR.m
M       cat_stat_ROI.m
M       cat_stat_TIV.m
M       cat_stat_check_cov.m
M       cat_surf_results.m
M       html/cat.html

(1) Changed: Check in cat_surf_results.m for empty cdata.
(2) Changed: Replaced xmltree by cat_io_xml in all functions.

------------------------------------------------------------------------
r1025 | dahnke | 2016-10-03 20:32:01 +0200 (Mon, 03 Oct 2016) | 23 lines

Changed paths:
M       CHANGES.txt
M       cat_main_LAS.m
M       cat_surf_createCS.m
M       development/cat_main_LAS.m
A  +    development/cat_surf_createCS.m
M       templates_1.50mm/cat.nii
M       templates_animals/ape_greater_T1.nii
M       templates_animals/ape_greater_T2.nii
!       templates_animals/ape_greater_TPMt.nii
M       templates_animals/ape_greater_brainmask.nii
M       templates_animals/ape_greater_vbm12.nii
M       templates_animals/monkey_oldworld_vbm12.nii

(1) Changed:  Refined human CAT atlas.
(2) Changed:  Refined greater apes CAT atlas.
(3) Changed:  Refined oldworld monkey CAT atlas.
(4) Changed:  Corrected Ypp estimation in "cat_main_LAS" to reduce problems
              with low quality images and old subjects.
(5) Changed:  Added further WMH correction in "development/cat_surf_createCS".



------------------------------------------------------------------------
r1024 | dahnke | 2016-10-01 18:37:22 +0200 (Sat, 01 Oct 2016) | 27 lines

Changed paths:
M       CHANGES.txt
MM      batches/cattest/cat12_SBM_101_segment.m
MM      batches/cattest/cat12_SBM_102_segment_greaterapes.m
MM      batches/cattest/cat12_SBM_103_segment_oldworldmonkeys.m
MM      batches/cattest/cat12_SBM_201_extractAddSurfPara.m
MM      batches/cattest/cat12_SBM_202_MapNormVol2AvgSurf.m
MM      batches/cattest/cat12_SBM_203_MapVol2IndSurf.m
MM      batches/cattest/cat12_SBM_204_ResampAndSmooth.m
MM      batches/cattest/cat12_SBM_301_Surf2ROI.m
MM      batches/cattest/cat12_SBM_302_exportRBM.m
M       cat_main_LAS.m
M       cat_surf_createCS.m
MM      cat_tst_cattest.m
M       development/cat_main_LAS.m
 M      html/cat_starting_cattest.html
 M      templates_1.50mm
M       templates_animals/ape_greater_vbm12.nii

(1) Changed:  Increased LAS GM sensitivity in "cat_main_LAS".
              This update will avoid blurred sulci in surface reconstruction
              but may lead to cuts in the parahippocampal gyrus!
(2) Changed:  Refined smoothing in "cat_surf_createCS" to reduce artifacts
              in noise data or by meninges.
(3) Changed:  Refined greater apes CAT atlas.


------------------------------------------------------------------------
r1023 | dahnke | 2016-09-30 17:19:46 +0200 (Fri, 30 Sep 2016) | 31 lines

Changed paths:
M       CHANGES.txt
M       batches/cattest/cat12_SBM_101_segment.m
M       batches/cattest/cat12_SBM_102_segment_greaterapes.m
M       batches/cattest/cat12_SBM_103_segment_oldworldmonkeys.m
M       batches/cattest/cat12_SBM_201_extractAddSurfPara.m
M       batches/cattest/cat12_SBM_202_MapNormVol2AvgSurf.m
M       batches/cattest/cat12_SBM_203_MapVol2IndSurf.m
M       batches/cattest/cat12_SBM_204_ResampAndSmooth.m
M       batches/cattest/cat12_SBM_301_Surf2ROI.m
M       batches/cattest/cat12_SBM_302_exportRBM.m
A       cat_roi_fun.m
M       cat_run_job.m
M       cat_stat_IQR.m
M       cat_stat_TIV.m
M       cat_surf_display.m
M       cat_surf_render.m
M       cat_surf_render2.m
M       cat_surf_vol2surf.m
M       cat_tst_cattest.m
!       development/cat.nii
MM      development/cat_main_LAS.m
M       internal/cat_io_volctype.m
M       templates_1.50mm/cat.nii

(1) Changed:  Small corrections in cat_stat_TIV.
(2) Changed:  Added "cat_vol_iscale" as function (is subfunction of 3 functions).
(3) Changed:  Added GUI, parameter test, and status report in "cat_tst_cattest".
(4) Checked:  All cattest batches can be loaded as matlab batch.
(5) Fixed:    Corrected miss-labeled regions in cat atlas.

------------------------------------------------------------------------
r1022 | gaser | 2016-09-29 23:10:38 +0200 (Thu, 29 Sep 2016) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_check_system_output.m
M       cat_conf_fmri.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_stat_spmT2x.m
M       cat_surf_info.m
M       cat_surf_results.m
M       cat_surf_vol2surf.m

(1) Changed: Updated cat_surf_results to allow more flexible file selection.
(2) Fixed: cat_surf_vol2surf.m gives now correct output names for batch mode.
(3) Fixed: cat_surf_info.m failed in getting an underlying mesh.
(4) Changed: Changed step size for vol2surf mapping.


------------------------------------------------------------------------
r1021 | dahnke | 2016-09-28 16:10:32 +0200 (Wed, 28 Sep 2016) | 33 lines

Changed paths:
M       CHANGES.txt
A       batches
A       batches/cattest
A       batches/cattest/cat12_SBM_101_segment.m
A       batches/cattest/cat12_SBM_102_segment_greaterapes.m
A       batches/cattest/cat12_SBM_103_segment_oldworldmonkeys.m
A       batches/cattest/cat12_SBM_201_extractAddSurfPara.m
A       batches/cattest/cat12_SBM_202_MapNormVol2AvgSurf.m
A       batches/cattest/cat12_SBM_203_MapVol2IndSurf.m
A       batches/cattest/cat12_SBM_204_ResampAndSmooth.m
A       batches/cattest/cat12_SBM_301_Surf2ROI.m
A       batches/cattest/cat12_SBM_302_exportRBM.m
M       cat_main_LAS.m
M       cat_run.m
M       cat_surf_parameters.m
M       cat_surf_surf2roi.m
M       cat_surf_vol2surf.m
A       cat_tst_cattest.m
A       cattest
M       development/cat_main_LAS.m
A       html/cat_starting_cattest.html
M       internal/cat_io_volctype.m
M       internal/cat_vol_reduceRes.m

(1) Changed:  Small correction for in "cat_run" and "cat_vol_reduceRes".
(2) Changed:  Automatic intensity scaling in "cat_io_volctype".
(3) New:      Added CAT processing example and test script "cat_tst_cattest"
              that used the SPM 2 mm Collins example scan for basic preprocessing.
(4) New:      Added "batches/cattest" directory that include the cattest scripts.
(5) New:      Prepared an unlinked HTML help page for "cat_tst_cattest".
(6) Fixed:    Corrected small error in "cat_main_LAS".

------------------------------------------------------------------------
r1020 | dahnke | 2016-09-26 14:46:28 +0200 (Mon, 26 Sep 2016) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_io_report.m
M       cat_main_LAS.m
M       cat_surf_vol2surf.m
M       cat_vol_defs.m
A  +    development/cat.nii
A       development/cat_main_LAS.m

{U+2248}(1) Changed*:   Update LAS cortex segmentation in "cat_main_LAS".
                Added further comments.
(2) Changed:    Added comments and verbose output in CAT deformation tool
                "cat_vol_defs". Refined regular expression of deformation
                file selector.
(3) Changed:    Refined ROI csv export
(4) Changed:    Small corrections in "cat_surf_vol2surf".


------------------------------------------------------------------------
r1019 | dahnke | 2016-09-26 08:41:05 +0200 (Mon, 26 Sep 2016) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_main.m
M       cat_stat_ROI.m
M       cat_surf_surf2roi.m
M       cat_vol_partvol.m

(1) Fixed:    Removed noise threshold for WMHC due to severe problems in SBM of
              OASIS_31.
(2) New:      GUI definition in "cat_conf_stools" for "cat_roi_parameter" to
              extract surface-based ROI measures.
(3) Changed:  Small corrections in "cat_conf_stools".
(4) Changed:  Changed ROI export in "cat_main" and "cat_stat_ROI".
(5) Changed:  Updated "cat_surf_surf2roi"


------------------------------------------------------------------------
r1018 | dahnke | 2016-09-25 13:25:41 +0200 (Sun, 25 Sep 2016) | 20 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_LAS.m
M       cat_surf_createCS.m
M       cat_surf_render2.m
M       cat_vol_pbt.m
M       cat_vol_resize.m
A       development

(1) Fixed:    Switched to a more selective filtering in "cat_vol_pbt" and added
              further noise reduction in "cat_vol_createCS" to reduce blurring
              of very small sulci.
(2) Fixed:    Removed tissue segmentation refinement by LAS that troubles the
              WMHC detection in "cat_main".
(3) Fixed:    Corrected error of the local intensity scaling in cat_main_LAS.
(4) Fixed:    Corrected problems in "cat_surf_render2".
(5) New:      Added "ROI" and "MenuBar" fields in "cat_surf_render2".


------------------------------------------------------------------------
r1017 | dahnke | 2016-09-23 07:55:23 +0200 (Fri, 23 Sep 2016) | 23 lines

Changed paths:
 M      .
M       CHANGES.txt
M       cat_check_system_output.m
M       cat_io_cprintf.m
M       cat_io_csv.m
A       cat_io_strrep.m
M       cat_io_xml.m
M       cat_surf_fun.m
M       cat_surf_gyrification.m

(1)  New*:      Added additional MAT-file read/write in "cat_io_xml" to increase
                reading speed of ROI data (1000 times faster).
(2)  New:       Added "cat_io_strrep" as more powerful version of strrep.
(3)  Fixed:     Small corrections in "cat_io_csv".
(4)  Changed:   Added "cdatamapping" and "cdatamappingtst" in "cat_surf_fun" to
                project data between different surfaces meshes using the spheres.
(5)  Changed:   In case of Laplacian GI estimation the hull surface is written
                persistently in "cat_surf_gyrification".
(6)  Changed:   Display help in case of empty input for "cat_io_cprintf".
(7)  Changed:   Corrected print string in "cat_check_system_output".


------------------------------------------------------------------------
r1016 | gaser | 2016-09-22 19:04:53 +0200 (Thu, 22 Sep 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_stat_spmF2x.m
M       cat_stat_spmT2x.m

Fixed: Transforming T-maps were not using an extent threshold for
surfaces (thanks to Michael Skeide for pointing to that bug).

------------------------------------------------------------------------
r1015 | gaser | 2016-09-22 18:01:50 +0200 (Thu, 22 Sep 2016) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m
M       cat_surf_results.m
M       cat_vol_groupwise_ls.m

(1) Fixed: Brainmask issue in longit. mode.
(2) Changed: Increased size of potential artefacts for TCA topology
    correction.


------------------------------------------------------------------------
r1014 | dahnke | 2016-09-22 16:28:17 +0200 (Thu, 22 Sep 2016) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_check_system_output.m
M       cat_io_FreeSurfer.m
M       cat_surf_info.m
M       cat_surf_smooth.m
M       cat_tst_qa_cleaner.m
M       internal/cat_example_surfsmooth.m

(1)  Fixed:      Corrected output of "cat_check_system_output".
(2)  Fixed:      Different processing for resampled data in "cat_surf_smooth".
(3)  Changed:    Updated help, parameter, and functions of "cat_tst_qa_cleaner".
(4)  Changed:    Updated "cat_surf_info" for hull surfaces (of GI measures).
(5)  Changed:    Updated help, error messages, and "gii2fs" and "fs2gii"
                 subfunctions in "cat_io_FreeSurfer".


------------------------------------------------------------------------
r1013 | dahnke | 2016-09-22 13:49:13 +0200 (Thu, 22 Sep 2016) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_main_gintnorm.m
M       cat_run.m
M       cat_run_job.m
M       html/cat_FAQ.html
M       internal/cat_example_surfsmooth.m

(1)  Fixed*:    Corrected wrong use of initial bias correction (APP=1) in
                "cat_run_job" that caused problems in the BWP.
(2)  Fixed:     Corrected problems in lazy segmentation in "cat_run"
                (development mode only).
(3)  Fixed:     Corrected noise estimation in "cat_main_gintnorm".
(4)  Changed:   Updated internal "cat_tst_qa_cleaner".
(5)  Changed:   Updated "cat_FAQ.html".


------------------------------------------------------------------------
r1012 | gaser | 2016-09-19 16:14:36 +0200 (Mon, 19 Sep 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat12.m

Fixed: Save SPM with default spm mat format.


------------------------------------------------------------------------
r1011 | gaser | 2016-09-19 03:48:41 +0200 (Mon, 19 Sep 2016) | 9 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       html/cat_starting.html

Changed: Slightly updated html and manual for ROI analysis.


------------------------------------------------------------------------
r1010 | gaser | 2016-09-18 19:13:49 +0200 (Sun, 18 Sep 2016) | 10 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
MM      cat_stat_analyze_ROIs.m
M       html/cat_methods_RBM.html

Changed: Updated html and manual for ROI analysis.


------------------------------------------------------------------------
r1009 | gaser | 2016-09-18 17:41:37 +0200 (Sun, 18 Sep 2016) | 11 lines

Changed paths:
M       CAT12-Manual.doc
M       CHANGES.txt
M       Contents.m
M       html/cat.html
M       html/cat_orthogonality.html
M       html/cat_starting.html

Changed: Updated quick starting guide wrt. to new ROI analysis.


------------------------------------------------------------------------
r1008 | gaser | 2016-09-18 17:18:24 +0200 (Sun, 18 Sep 2016) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat12.fig
M       cat12.m
A       cat_stat_analyze_ROIs.m
M       cat_surf_results.m
M       html/cat_starting.html

(1) Added: Function to analyze ROI data cat_stat_analyze_ROIs.m.
(2) Changed: GUI to add ROI analysis.
(3) Changed: Updated comments and functionality of cat_surf_results.m.

------------------------------------------------------------------------
r1007 | gaser | 2016-09-18 17:08:03 +0200 (Sun, 18 Sep 2016) | 18 lines

Changed paths:
M       CHANGES.txt
A  +    atlases_surfaces/a2005s.txt
        > moved from atlases_surfaces_not_distributed/a2005s.txt
D       atlases_surfaces/pals.txt
        > moved to atlases_surfaces_not_distributed/pals.txt
D       atlases_surfaces_not_distributed/a2005s.txt
        > moved to atlases_surfaces/a2005s.txt
A  +    atlases_surfaces_not_distributed/pals.txt
        > moved from atlases_surfaces/pals.txt
M       html/cat_methods_RBM.html
M       html/cat_orthogonality.html
M       html/cat_starting.html

(1) Fixed: Updated html code for atlases according to DK40 atlas.
(2) Changed: Added description for DK40 atlas to atlas_surfaces.
(3) Changed: Added hint to center TIV as covariate.

------------------------------------------------------------------------
r1006 | gaser | 2016-09-15 00:11:41 +0200 (Thu, 15 Sep 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat12.fig
M       cat_surf_results.m

(1) Fixed: Empty output by calling cat_surf_results.m is now prevented.
(2) Changed: Added flag to disable warning about filenames in
    cat_surf_results.m


------------------------------------------------------------------------
r1005 | gaser | 2016-09-14 13:50:17 +0200 (Wed, 14 Sep 2016) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_ROI.m
M       cat_surf_results.m
M       html/cat.html

(1) Changed: Added ROIid to ROI stat.
(2) Changed: Changed enabling of threshold selection slightly to allow more
    flexibility.


------------------------------------------------------------------------
r1004 | gaser | 2016-09-14 04:01:12 +0200 (Wed, 14 Sep 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_results.m
M       html/cat.html

Fixed: Wrong atlas name was used in cat_surf_results.m because atlas names chaged.


------------------------------------------------------------------------
r1003 | gaser | 2016-09-13 04:25:42 +0200 (Tue, 13 Sep 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_ROI.m
M       html/cat.html

Fixed: Removed again compatibility issues in cat_stat_ROI.m


------------------------------------------------------------------------
r1002 | gaser | 2016-09-12 10:18:35 +0200 (Mon, 12 Sep 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       html/cat.html

Fixed: Changed call of TFCE toolbox that sometimes prevented use
functionality of results section.


------------------------------------------------------------------------
r1001 | gaser | 2016-09-12 03:25:34 +0200 (Mon, 12 Sep 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat12.fig
M       cat12.m
M       cat_vol_groupwise_ls.m

(1) Changed: Added menu for downloading TFCE toolbox if not yet installed.
(2) Fixed: Some issues in cat_vol_groupwise_ls.m if no initial brainmask
    was used.

------------------------------------------------------------------------
r1000 | gaser | 2016-09-09 15:11:35 +0200 (Fri, 09 Sep 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_defs.m

Fixed: In cat_vol_defs now also img files can be processed and not only nii.


------------------------------------------------------------------------
r999 | gaser | 2016-09-08 04:26:32 +0200 (Thu, 08 Sep 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       html/cat.html

Changed: Added option to deselect APP in default mode.


------------------------------------------------------------------------
r998 | gaser | 2016-09-07 08:39:01 +0200 (Wed, 07 Sep 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_ROI.m
M       html/cat.html

Fixed: Added check for writing permissions in cat_stat_ROI.m.


------------------------------------------------------------------------
r997 | gaser | 2016-09-07 07:59:07 +0200 (Wed, 07 Sep 2016) | 17 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
A  +    atlases_surfaces/lh.aparc_DK40.freesurfer.annot
D       atlases_surfaces/lh.aparc_freesurfer.annot
A  +    atlases_surfaces/rh.aparc_DK40.freesurfer.annot
D       atlases_surfaces/rh.aparc_freesurfer.annot
M       cat_conf_stools.m
M       cat_surf_surf2roi.m
M       cat_update.m
M       html/cat.html

(1) Changed: Also delete old atlas files during update.
(2) Fixed: ROI estimation for surfaces was not yet correctly working.
(3) Changed: Renamed aparc_freesurfer atlas to aparc_DK40 atlas.


------------------------------------------------------------------------
r996 | gaser | 2016-09-07 06:53:36 +0200 (Wed, 07 Sep 2016) | 6 lines

Changed paths:
M       CHANGES.txt

Changed: Updated cat_surf_results.m to also show plots of fitted data.


------------------------------------------------------------------------
r995 | gaser | 2016-09-07 06:52:40 +0200 (Wed, 07 Sep 2016) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_results.m
M       html/cat.html

(1) Changed: Moved most atlases to a folder that is not distributed.
(2) Changed: Use aparc_freesurfer instead of aparc_DKT40JT until inconsistencies
    between the regions (banksst) are corrected.



------------------------------------------------------------------------
r994 | gaser | 2016-09-07 04:31:30 +0200 (Wed, 07 Sep 2016) | 62 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
D       atlases_surfaces/a2005s.txt
D       atlases_surfaces/dkt40.txt
D       atlases_surfaces/lh.PALS_B12_Brodmann.freesurfer.annot
D       atlases_surfaces/lh.PALS_B12_Lobes.freesurfer.annot
D       atlases_surfaces/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
D       atlases_surfaces/lh.PALS_B12_Visuotopic.freesurfer.annot
D       atlases_surfaces/lh.aal.Template_T1_IXI555_MNI152
D       atlases_surfaces/lh.aparc_DKT40JT.freesurfer.annot
D       atlases_surfaces/lh.aparc_a2005s.freesurfer.annot
D       atlases_surfaces/lh.hammers.Template_T1_IXI555_MNI152
D       atlases_surfaces/lh.lpba40.Template_T1_IXI555_MNI152
D       atlases_surfaces/lh.mori.Template_T1_IXI555_MNI152
D       atlases_surfaces/lh.neuromorphometrics.Template_T1_IXI555_MNI152
D       atlases_surfaces/rh.PALS_B12_Brodmann.freesurfer.annot
D       atlases_surfaces/rh.PALS_B12_Lobes.freesurfer.annot
D       atlases_surfaces/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
D       atlases_surfaces/rh.PALS_B12_Visuotopic.freesurfer.annot
D       atlases_surfaces/rh.aal.Template_T1_IXI555_MNI152
D       atlases_surfaces/rh.aparc_DKT40JT.freesurfer.annot
D       atlases_surfaces/rh.aparc_a2005s.freesurfer.annot
D       atlases_surfaces/rh.hammers.Template_T1_IXI555_MNI152
D       atlases_surfaces/rh.lpba40.Template_T1_IXI555_MNI152
D       atlases_surfaces/rh.mori.Template_T1_IXI555_MNI152
D       atlases_surfaces/rh.neuromorphometrics.Template_T1_IXI555_MNI152
A       atlases_surfaces_not_distributed
A  +    atlases_surfaces_not_distributed/DKT40JT.txt
A  +    atlases_surfaces_not_distributed/a2005s.txt
A  +    atlases_surfaces_not_distributed/lh.PALS_B12_Brodmann.freesurfer.annot
A  +    atlases_surfaces_not_distributed/lh.PALS_B12_Lobes.freesurfer.annot
A  +    atlases_surfaces_not_distributed/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
A  +    atlases_surfaces_not_distributed/lh.PALS_B12_Visuotopic.freesurfer.annot
A  +    atlases_surfaces_not_distributed/lh.aal.Template_T1_IXI555_MNI152
A  +    atlases_surfaces_not_distributed/lh.aparc_DKT40JT.freesurfer.annot
A  +    atlases_surfaces_not_distributed/lh.aparc_a2005s.freesurfer.annot
A  +    atlases_surfaces_not_distributed/lh.hammers.Template_T1_IXI555_MNI152
A  +    atlases_surfaces_not_distributed/lh.lpba40.Template_T1_IXI555_MNI152
A  +    atlases_surfaces_not_distributed/lh.mori.Template_T1_IXI555_MNI152
A  +    atlases_surfaces_not_distributed/lh.neuromorphometrics.Template_T1_IXI555_MNI152
A  +    atlases_surfaces_not_distributed/rh.PALS_B12_Brodmann.freesurfer.annot
A  +    atlases_surfaces_not_distributed/rh.PALS_B12_Lobes.freesurfer.annot
A  +    atlases_surfaces_not_distributed/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
A  +    atlases_surfaces_not_distributed/rh.PALS_B12_Visuotopic.freesurfer.annot
A  +    atlases_surfaces_not_distributed/rh.aal.Template_T1_IXI555_MNI152
A  +    atlases_surfaces_not_distributed/rh.aparc_DKT40JT.freesurfer.annot
A  +    atlases_surfaces_not_distributed/rh.aparc_a2005s.freesurfer.annot
A  +    atlases_surfaces_not_distributed/rh.hammers.Template_T1_IXI555_MNI152
A  +    atlases_surfaces_not_distributed/rh.lpba40.Template_T1_IXI555_MNI152
A  +    atlases_surfaces_not_distributed/rh.mori.Template_T1_IXI555_MNI152
A  +    atlases_surfaces_not_distributed/rh.neuromorphometrics.Template_T1_IXI555_MNI152
M       cat_conf_stools.m
M       cat_surf_surf2roi.m
M       html/cat.html

(1) Changed: Moved most atlases to a folder that is not distributed.
(2) Changed: Use aparc_freesurfer instead of aparc_DKT40JT until inconsistencies
    between the regions (banksst) are corrected.



------------------------------------------------------------------------
r993 | gaser | 2016-09-02 18:38:40 +0200 (Fri, 02 Sep 2016) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_ROI.m
M       html/cat.html

Fixed: Error in cat_stat_ROI.m that was caused due to wrong compatibility
to older versions.



------------------------------------------------------------------------
r992 | gaser | 2016-09-02 11:42:40 +0200 (Fri, 02 Sep 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_surf2roi.m
M       html/cat.html

Fixed: Error in cat_surf_surf2roi.m that was caused due to wrong writing flag.



------------------------------------------------------------------------
r991 | gaser | 2016-08-31 22:29:40 +0200 (Wed, 31 Aug 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_parameters.m

Fixed: Error in cat_surf_parameter due to developer options.


------------------------------------------------------------------------
r990 | gaser | 2016-08-31 14:16:22 +0200 (Wed, 31 Aug 2016) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat12.fig
M       cat12.m
M       cat_stat_check_cov.m
MM      cat_surf_results.m

(1) Changed: Updated cat_surf_results with many more options.
(2) Changed: Threshold for equal data in cat_stat_check_cov.m is now
    increased to 09.25.
(3) Added: Added surface results tool to GUI.

------------------------------------------------------------------------
r989 | gaser | 2016-08-29 13:41:13 +0200 (Mon, 29 Aug 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_results.m
M       html/cat.html

Changed: Updated cat_surf_results with more options.

------------------------------------------------------------------------
r988 | gaser | 2016-08-26 17:45:09 +0200 (Fri, 26 Aug 2016) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
A       cat_surf_results.m
M       html/cat.html
M       templates_surfaces/lh.inflated.freesurfer.gii
M       templates_surfaces/rh.inflated.freesurfer.gii

(1) Added: cat_surf_results for overlaying surface results with multiple views.
(2) Fixed: Left and right inflated hemispheres overlapped spatially.

------------------------------------------------------------------------
r987 | gaser | 2016-08-23 16:49:59 +0200 (Tue, 23 Aug 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_calc.m

Fixed: Defined outdir was not used in cat_surf_calc.m.

------------------------------------------------------------------------
r986 | gaser | 2016-08-23 16:40:46 +0200 (Tue, 23 Aug 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat12.fig
M       cat12.m
M       cat_surf_display.m

Changed: Corrected typos in cat_surf_display and changed default colormap
to jet for non-expert mode.


------------------------------------------------------------------------
r985 | gaser | 2016-08-18 10:08:34 +0200 (Thu, 18 Aug 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat12.fig
M       cat_stat_ROI.m
M       cat_surf_surf2roi.m

(1) Fixed: Corrected typos in cat12-GUI.
(2) Fixed: Updated ROI tools that now also work for surfaces correctly.

------------------------------------------------------------------------
r984 | gaser | 2016-08-17 12:39:46 +0200 (Wed, 17 Aug 2016) | 9 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       html/cat.html

Changed: Updated CAT12-manual.

------------------------------------------------------------------------
r983 | gaser | 2016-08-12 08:29:53 +0200 (Fri, 12 Aug 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       spm_cat12.m

Changed: Removed some (only internally used) paths form the dirlist in spm_cat12.m.

------------------------------------------------------------------------
r982 | dahnke | 2016-08-09 17:18:00 +0200 (Tue, 09 Aug 2016) | 24 lines

Changed paths:
M       CHANGES.txt
M       cat_io_cprintf.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_run_job.m
M       cat_surf_fun.m
M       cat_surf_render2.m
M       cat_tst_calc_kappa.m
M       cat_vol_isarnlm.m
M       spm_cat12.m

(1) Fixed*:     Corrected error in ISARNLM filter that avoid filtering low
                resolution filtering of ultra-highres images.
(2) Fixed*:     Corrected problems in LAS in ultra-highres images.
(3) Fixed*:     Corrected AMAP problem in  ultra-highres images by resolution
                adaptive sub-parameter and improved CSF background.
(4) Fixed*:     Corrected call of 3rd noise correction after LAS.
(5) Changed:    Updated cat_tst_calc_kappa for GM expert segment data.
(5) Changed:    Added CAT main directories in SPM directory list.
(6) Changed:    Added manual reset of color output in cat_io_cprintf.



------------------------------------------------------------------------
r981 | gaser | 2016-08-09 15:04:05 +0200 (Tue, 09 Aug 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_resamp.m

Fixed: Path of filename in gifti-metadata is now removed after resampling.
This alllows to move the resampled files.

------------------------------------------------------------------------
r980 | gaser | 2016-08-09 12:01:46 +0200 (Tue, 09 Aug 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_check_cov.m
M       html/cat.html

Fixed: Order of filenames after switching plot is now correct.

------------------------------------------------------------------------
r979 | gaser | 2016-08-08 16:21:16 +0200 (Mon, 08 Aug 2016) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_long_main.m
M       cat_surf_resamp.m
M       html/cat.html
M       templates_1.50mm/hammers.csv
M       templates_1.50mm/labels_dartel_hammers.xml
M       templates_1.50mm/labels_dartel_mori.xml
M       templates_1.50mm/labels_dartel_neuromorphometrics.xml
M       templates_1.50mm/mori.csv
M       templates_1.50mm/neuromorphometrics.csv

(1) Changed: Resampled surfaces have less artefacts due to resampling.
(2) Fixed: Corrected some anatomical names in atlases.

------------------------------------------------------------------------
r978 | gaser | 2016-08-08 11:32:11 +0200 (Mon, 08 Aug 2016) | 11 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_conf_opts.m
M       cat_conf_stools.m
M       html/images/non_orthogonal.png

(1) Changed: Moved some options to expert mode
(2) Fixed: Non-orthogonality image is now fixed in manual and help.

------------------------------------------------------------------------
r977 | gaser | 2016-08-01 19:14:38 +0200 (Mon, 01 Aug 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_groupwise_ls.m

Fixed: Realigned images using cat_vol_groupwise_ls.m have now correct (flipped)
x-voxel size (thanks to Paul Schmidt for pointing to that issue).

------------------------------------------------------------------------
r976 | dahnke | 2016-08-01 18:14:59 +0200 (Mon, 01 Aug 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_render.m
M       cat_surf_render2.m

(1) Changed:    Corrected error in old cat_surf_render function.

------------------------------------------------------------------------
r975 | dahnke | 2016-08-01 17:49:47 +0200 (Mon, 01 Aug 2016) | 28 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_io_FreeSurfer.m
M       cat_io_report.m
M       cat_main.m
M       cat_run_job.m
M       cat_run_job_APP_final.m
M       cat_surf_display.m
M       cat_surf_render.m
A  +    cat_surf_render2.m
M       cat_vol_div.m
M       internal/cat_tst_prepareManualSegmentation.m
M       spm_cat12.m

(1) Changed:    Due to further problems with surface rendering the improved
                cat_surf_render function cat_surf_render2 is only called in
                developer mode.
(2) Fixed:      Corrected errors in cat_surf_render.
(3) Changed:    Updated help entry in cat12 and spm_cat12.
(4) Fixed:      Corrected error in error report. The histogram colors are not
                correct in some images (more test required).
(5) Fixed:      Corrected error in cat_run_job_APP_final with incorrect mask
                for threshold estimation.
(6) Changed:    Improved volume render function in cat_surf_render.
(7) Added:      Added FreeSurfer annot-export function.


------------------------------------------------------------------------
r974 | gaser | 2016-07-27 11:05:07 +0200 (Wed, 27 Jul 2016) | 10 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_vol_slice_overlay.m
M       html/cat.html

Fixed: Range in cat_vol_slice_overlay.m was not correctly handled.

------------------------------------------------------------------------
r973 | gaser | 2016-07-25 11:58:38 +0200 (Mon, 25 Jul 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       html/cat.html

Fixed: Normalized Jacobian dets were just named j_* without leading "w".

------------------------------------------------------------------------
r972 | gaser | 2016-07-25 11:30:44 +0200 (Mon, 25 Jul 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
M       html/cat.html

Fixed: Metadata after resampling and smoothing now only contain name and not
path of the filename to allow that files can be moved before stat. analysis.

------------------------------------------------------------------------
r971 | gaser | 2016-07-22 14:34:56 +0200 (Fri, 22 Jul 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_run.m
M       tbx_cfg_cat.m

Fixed: Corrected handling and fields for las output.

------------------------------------------------------------------------
r970 | gaser | 2016-07-22 12:56:01 +0200 (Fri, 22 Jul 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_render.m
M       html/cat.html

Fixed: cat_surf_render did not work properly for all matlab version, now use
old version again.

------------------------------------------------------------------------
r969 | dahnke | 2016-07-21 14:34:10 +0200 (Thu, 21 Jul 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m

(1) Fixed:      Volume creation error in TCA part of cat_surf_createCS (part 2).


------------------------------------------------------------------------
r968 | dahnke | 2016-07-21 14:32:02 +0200 (Thu, 21 Jul 2016) | 51 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_main_gintnorm.m
M       cat_surf_createCS.m
M       cat_surf_render.m
M       cat_surf_resamp.m
M       internal/cat_tst_prepareManualSegmentation.m
M       tbx_cfg_cat.m
M       templates_animals/ape_greater_T1.nii
M       templates_animals/ape_greater_T2.nii
M       templates_animals/ape_greater_TPM.nii
M       templates_animals/ape_greater_TPMt.nii
M       templates_animals/ape_greater_Template_1.nii
M       templates_animals/ape_greater_Template_2.nii
M       templates_animals/ape_greater_Template_3.nii
M       templates_animals/ape_greater_Template_4.nii
M       templates_animals/ape_greater_Template_5.nii
M       templates_animals/ape_greater_Template_6.nii
M       templates_animals/ape_greater_brainmask.nii
M       templates_animals/ape_greater_vbm12.nii
M       templates_animals/monkey_oldworld_T1.nii
M       templates_animals/monkey_oldworld_T2.nii
M       templates_animals/monkey_oldworld_TPM.nii
M       templates_animals/monkey_oldworld_Template_1.nii
M       templates_animals/monkey_oldworld_Template_2.nii
M       templates_animals/monkey_oldworld_Template_3.nii
M       templates_animals/monkey_oldworld_Template_4.nii
M       templates_animals/monkey_oldworld_Template_5.nii
M       templates_animals/monkey_oldworld_Template_6.nii
M       templates_animals/monkey_oldworld_brainmask.nii
M       templates_animals/monkey_oldworld_vbm12.nii

(1) Changed:    Separate the bias, noise and intensity corrected image (Ym)
                into two subversion with global (Ym) and local (Ymi) intensity
                normalization. The Ym is more reasonable for myelination
                analysis, whereas the Ymi more sensible for the tissue classes.
                Also for Ym LAS is used to correct reminding WM inhomogeneities.
                The output of the local normalized image is only assessable via
                cat_defaults (cat.output.las) and expert GUI.
                The CAT ROIs will extract the intensities of the Ym rather of
                the Ymi. The CAT report now shows the Ym rather than the Ymi.
(2) Changed:    Added ROI menu to expert GUI.
(3) Fixed:      Volume creation error in TCA part of cat_surf_createCS.
(4) Fixed:      Update version of cat_surf_render.
(5) Changed:    Added surface type check in cat_surf_resamp to ignore
                '.central.' and '.sphere.'.
(6) Fixed:      Fast correction of side flip in animal atlas maps.

------------------------------------------------------------------------
r967 | gaser | 2016-07-21 10:50:05 +0200 (Thu, 21 Jul 2016) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_spmT2x.m
M       cat_surf_display.m
M       cat_surf_render.m
M       html/cat.html

(1) Fixed: cat_stat_spmT2x.m failed in reading RPV.gii.
(2) Changed: Added differentation for expert mode in cat_surf_display to only
    show .gii files for non-experts.

------------------------------------------------------------------------
r966 | gaser | 2016-07-20 16:40:20 +0200 (Wed, 20 Jul 2016) | 10 lines

Changed paths:
M       CHANGES.txt
MM      cat_io_mergeStruct.m
M       cat_stat_ROI.m
M       cat_surf_render.m
 M      internal/cat_example_surfsmooth.m
MM      internal/cat_tst_prepareManualSegmentation.m

Fixed: cat_stat_ROI.m can now handle volume and surface data at the same time.

------------------------------------------------------------------------
r965 | gaser | 2016-07-20 15:44:09 +0200 (Wed, 20 Jul 2016) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_spmF2x.m
M       cat_stat_spmT2x.m
M       cat_surf_info.m
M       html/cat.html

(1) Fixed: cat_stat_spmT2x.m did not worked for surfaces.
(2) Changed: Added check for existing SPM.mat to cat_surf_info.m to get
    side info.
(3) Fixed: H.colourbar.Limits did not exist in cat_surf_render.m

------------------------------------------------------------------------
r964 | dahnke | 2016-07-20 15:42:29 +0200 (Wed, 20 Jul 2016) | 47 lines

Changed paths:
M       CHANGES.txt
M       cat_check_system_output.m
M       cat_conf_stools.m
M       cat_get_defaults.m
M       cat_io_FreeSurfer.m
A       cat_io_mergeStruct.m
M       cat_surf_display.m
M       cat_surf_fun.m
M       cat_surf_info.m
M       cat_surf_parameters.m
M       cat_surf_render.m
M       cat_surf_smooth.m
M       cat_surf_surf2roi.m
M       cat_surf_vol2surf.m
M       cat_version.m
M       cat_vol_isarnlm.m
A       internal/cat_example_surfsmooth.m
A       internal/cat_tst_prepareManualSegmentation.m
M       spm_cat12.m
M       tbx_cfg_cat.m

(1) Changed*:  Updated cat_surf_render:
               - Changed menu field order and field names.
               - Add print resolution option (DPI).
               - Corrected CAM lighting.
               - Added texture menu to load other maps of the same subject.
               - Added mesh menu to load other meshes of the same subject/average.
               - Reduced number of colormaps, but added an invertation function.
(2) Add*:      Added the internal script cat_tst_prepareManualSegmentation that
               prepare an initial tissue classification for manual corrections
               to obtain ground truth data.
               It creates images that are corrected for noise, inhomogeneity
               and contrast, and writes a volume with a set of slices with an
               initial labeling based on the corrected input image.
(3) Fixed*:    Updated cat_surf_smooth for GIFTI input and alternative smoothing
               (spm_mesh_smooth) in cat_surf_smooth. Added internal script
               cat_example_surfsmooth to compare volume and surface smoothing.
(4) Fixed:     Corrected small errors in cat_check_system_output,
               cat_io_FreeSurfer, cat_surf_display, cat_surf_info.
(5) Changed:   Delete functions and output for cat_get_defaults.
(6) Changed:   Added CAT banner in cat_versions.
(7) Changed:   Added some further comments in cat_surf_surf2roi, tbx_cfg_cat
               and vol2surf.
(8) Add:       In preparation: ROI output for surface measures.


------------------------------------------------------------------------
r963 | gaser | 2016-07-18 15:48:14 +0200 (Mon, 18 Jul 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       html/cat.html
M       html/cat.txt

Fixed: Wrong (old) release number was shwon in html pages.

------------------------------------------------------------------------
r962 | dahnke | 2016-06-24 13:30:56 +0200 (Fri, 24 Jun 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_render.m

(1) Fixed:    Updated cat_surf_render function.


------------------------------------------------------------------------
r961 | gaser | 2016-06-24 11:30:22 +0200 (Fri, 24 Jun 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_render.m

Changed: Removed filename in windows in cat_surf_render.m

------------------------------------------------------------------------
r960 | dahnke | 2016-06-24 09:51:08 +0200 (Fri, 24 Jun 2016) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_io_FreeSurfer.m
M       cat_io_report.m
M       cat_main.m
M       cat_surf_display.m
M       cat_surf_info.m
M       cat_surf_render.m

(1) Fixed*:   Updated SPM segmentation handling in cat_main.
(2) Fixed:    Updated cat_surf_render function.


------------------------------------------------------------------------
r959 | gaser | 2016-06-23 11:23:32 +0200 (Thu, 23 Jun 2016) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_check_system_output.m
M       cat_conf_stools.m
M       cat_run.m
M       cat_surf_render.m
M       cat_surf_surf2roi.m
M       tbx_cfg_cat.m

(1) Fixed: Error in cat_surf_surf2roi.m because of missing fieldname.
(2) Fixed: Parallel mode is disabled in deploayed mode.
(3) Changed: Added underlay function and some more functionality to
    cat_surf_render.m
(4) Fixed: Missing filed in cat_run.m if other DARTEl template was chosen.

------------------------------------------------------------------------
r958 | gaser | 2016-06-21 17:22:38 +0200 (Tue, 21 Jun 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_check_system_output.m

Fixed: Error in cat_check_system_output.m due to special characters
       under windows.

------------------------------------------------------------------------
r957 | gaser | 2016-06-21 13:10:46 +0200 (Tue, 21 Jun 2016) | 11 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_io_xml.m
M       cat_main.m
M       html/cat_methods_RBM.html

(1) Changed: Updated manual.
(2) Fixed: Error with flipped colorbars.

------------------------------------------------------------------------
r956 | gaser | 2016-06-21 10:27:19 +0200 (Tue, 21 Jun 2016) | 12 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
MM      cat_stat_ROI.m
M       html/cat_methods_RBM.html
M       tbx_cfg_cat.m

Changed: Updated html text and manual.

------------------------------------------------------------------------
r955 | gaser | 2016-06-20 22:39:15 +0200 (Mon, 20 Jun 2016) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_long.m
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_long_main.m
M       cat_long_multi_run.m
M       cat_main.m

Changed: Added option to save dartel exported images in longitudinal batch.

------------------------------------------------------------------------
r954 | dahnke | 2016-06-20 12:44:20 +0200 (Mon, 20 Jun 2016) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stoolsexp.m
M       cat_io_report.m
M       cat_main.m
M       cat_surf_display.m
M       cat_surf_render.m
M       cat_tst_qa_cleaner.m

(1) Fixed:   Corrected CAT report colormap problem (blue brain) in case of
             surface reconstruction.
(2) Changed: Color histogram in error report.

------------------------------------------------------------------------
r953 | gaser | 2016-06-18 14:52:36 +0200 (Sat, 18 Jun 2016) | 48 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
D       atlases_surfaces/lh.aparc_DKT40.freesurfer.annot
D       atlases_surfaces/rh.aparc_DKT40.freesurfer.annot
M       cat12.fig
M       cat12.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_main.m
A       cat_stat_ROI.m
M       cat_surf_createCS.m
M       cat_surf_surf2roi.m
D       cat_surf_surf2roi_resampled.m
M       cat_surf_vol2surf.m
M       cat_vol_atlas.m
M       cat_vol_partvol.m
M       html/cat_methods_RBM.html
 M      html/cat_orthogonality.html
 M      html/images/non_orthogonal.png
M       internal/cat_vol_atlas.m
M       spm_cat12.m
M       templates_1.50mm/aal.csv
M       templates_1.50mm/anatomy.csv
M       templates_1.50mm/cat.nii
M       templates_1.50mm/cobra.csv
M       templates_1.50mm/hammers.csv
M       templates_1.50mm/ibsr.csv
M       templates_1.50mm/lpba40.csv
M       templates_1.50mm/mori.csv
M       templates_1.50mm/neuromorphometrics.csv

(1) Changed: Changed again topology correction that now uses tca in gyrus
    parahippocampalis and hippocampus as default.
(2) Changed: Updated CAT12 manual and html code (ROI analysis)
(3) Added: ROI extraction and estimation
(4) Removed: DKT40 atlas (DKT40JT is updated version).
(5) Changed: Added gyrus parahippocampalis to cat-atlas.
(6) Fixed: Bug in spm_cat12 with isempty
(7) Fixed: Bug in cat_surf_vol2surf with mapping flag.
(8) Removed: cat_surf_surf2roi_resampled.m
(9) Fixed: Bug in cat_surf_surf2roi with rdata field
(10) Changed: Removed csv output of ROIs for each dataset (only one xml file
     are saved)

------------------------------------------------------------------------
r952 | dahnke | 2016-06-15 14:15:01 +0200 (Wed, 15 Jun 2016) | 33 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_conf_extopts.m
M       cat_io_senderrormail.m
M       cat_main_gcut.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job_APP_final.m
M       cat_vol_correct_slice_scaling.m
M       cat_vol_morph.m
M       spm_cat12.m
D       templates_animals/ape_lesser_T1.nii
D       templates_animals/ape_lesser_T2.nii
D       templates_animals/ape_lesser_TPM.nii
D       templates_animals/ape_lesser_brainmask.nii
D       templates_animals/cat_defaults_ape_greater.m
D       templates_animals/cat_defaults_ape_lesser.m
D       templates_animals/cat_defaults_monkey_newworld.m
D       templates_animals/cat_defaults_monkey_oldworld.m
D       templates_animals/monkey_newworld_T1.nii
D       templates_animals/monkey_newworld_T2.nii
D       templates_animals/monkey_newworld_TPM.nii
D       templates_animals/monkey_newworld_brainmask.nii

(1) Changed:  Updated help of spm_cat12.
(2) Changed:  Updated main head classification in final APP increase the chance
              to remove the scull and not the brain in species with thick muscles.
(3) Changed:  Small corrections.
(4) Deleted:  Removed species specific default files and set parameter in spm_cat12.
(5) Deleted:  Removed incomplete species templates.


------------------------------------------------------------------------
r951 | gaser | 2016-06-15 13:33:16 +0200 (Wed, 15 Jun 2016) | 6 lines

Changed paths:
M       CHANGES.txt

(1) Changed: Added description about design orthogonality to CAT12 manual.
(2) Added: html page about design orthogonality

------------------------------------------------------------------------
r950 | gaser | 2016-06-15 13:33:03 +0200 (Wed, 15 Jun 2016) | 12 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
MM      cat_tst_qa_cleaner.m
A       html/cat_orthogonality.html
M       html/cat_starting.html
A       html/images/non_orthogonal.png

(1) Changed: Added description about design orthogonality to CAT12 manual.
(2) Added: html page about design orthogonality

------------------------------------------------------------------------
r949 | dahnke | 2016-06-13 15:34:18 +0200 (Mon, 13 Jun 2016) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_main.m
M       cat_tst_qa.m
M       cat_tst_qa_cleaner.m
M       tbx_cfg_cat.m
M       templates_animals/cat_defaults_ape_greater.m
M       templates_animals/cat_defaults_ape_lesser.m
M       templates_animals/cat_defaults_monkey_newworld.m
M       templates_animals/cat_defaults_monkey_oldworld.m

(1) Changed:  Updated comments of intensity-based tissue class output maps (pi*)
              (developer mode).
(2) Changed:  Removed TE (tissue expectation) and PC (preprocessing change) maps
              completely.

------------------------------------------------------------------------
r948 | gaser | 2016-06-08 17:01:56 +0200 (Wed, 08 Jun 2016) | 21 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_surf_createCS.m
M       cat_surf_epivolsurf.m
M       cat_surf_surf2roi.m
M       cat_surf_surf2roi_resampled.m
M       cat_vol_partvol.m
M       html/cat_methods_RBM.html

(1) Fixed: Some typos and missing svn ID fields in header
(2) Changed: Surface creation is now starting with the good old topology
    correction and will check whether the Hausdorff distance in the
    parahippocampal gyrus will be too large. In that case a new run with
    BrainSuite topology correction (tca) is made to prevent large cuts in that
    gyrus.
(3) Changed: Topology correction is now also internally using criteria of
    Haussdorff distance multiplied with mean curvature to decide whether
    the defect is a hole or handle.

------------------------------------------------------------------------
r947 | dahnke | 2016-06-08 16:42:37 +0200 (Wed, 08 Jun 2016) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_io_senderrormail.m
M       cat_plot_boxplot.m
A       cat_tst_qa_cleaner.m
M       cat_vol_findfiles.m

New:      Added a function cat_tst_qa_cleaner to estimate a sample specific QA
          threshold of a set of quality ratings. It used the kmeans function to
          find the first peak and the average variation to get a sample specific
          QA rating with 2 major levels (passed/failed) and 2 refinements (+/-).


------------------------------------------------------------------------
r946 | gaser | 2016-06-06 17:17:45 +0200 (Mon, 06 Jun 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat12.fig
M       cat12.m

Fixed: TFCE call from GUI

------------------------------------------------------------------------
r945 | gaser | 2016-06-06 08:54:56 +0200 (Mon, 06 Jun 2016) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_roi_roi2surf.m
 M      cat_surf_GI3D.m
 M      cat_surf_epivolsurf.m
MM      cat_surf_fun.m
MM      cat_surf_gyrification.m
M       cat_surf_parameters.m
MM      internal/cat_io_volctype.m

(1) Fixed: Check of flag for new surface parameters are only available in
    expert mode.
(2) Fixed: Typos and wrong file subversion IDs.



------------------------------------------------------------------------
r944 | dahnke | 2016-05-31 17:06:45 +0200 (Tue, 31 May 2016) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
D       cat_defaults_expert.m
M       html/cat_methods_RBM.html
M       html/cat_methods_defaults.html
M       spm_cat12.m

Changed:  Removed cat_defaults_expert file.
Changed:  Reduced atlas files in HTML help.
Changed:  Improved call and display of default/expert/developer GUI.

------------------------------------------------------------------------
r943 | gaser | 2016-05-31 12:05:09 +0200 (Tue, 31 May 2016) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_display.m
M       cat_surf_fun.m
M       cat_surf_gyrification.m

(1) Changed: Corrected many typos from last release.
(2) Fixed: Error in cat_surf_display for dispolaying multiple surfaces.



------------------------------------------------------------------------
r942 | dahnke | 2016-05-30 14:49:42 +0200 (Mon, 30 May 2016) | 35 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_io_updateStruct.m
M       cat_stat_marks.m
A       cat_surf_GI3D.m
A       cat_surf_epivolsurf.m
A       cat_surf_fun.m
A       cat_surf_gyrification.m
M       cat_surf_info.m
M       cat_surf_parameters.m
M       cat_surf_render.m
M       cat_tst_qa.m
A       internal/cat_io_volctype.m
M       kmeans3D.m

Fixed:    Small corrections in cat_tst_qa and cat_stat_marks for direct calls
          e.g. for other input segmentations.
Fixed:    Corrected small errors in cat_io_updateStruct.
Changed:  Small updates of cat_surf_info for display hull surface.
Changed:  Further output of kmeans3D.
Changed:  Added expert GI functions in cat_surf_parameter.
New:      Added cat_surf_gyrification as collection of different surface
          relation based gyrification measures.
          (central vs. sphere/inflate/average/laplace).
New:      Added cat_surf_fun as collection of small surface functions that are
          required for further cortical measures such as the GI, that include
          area estimation, hull creation for surfaces, and volume rendering.
New:      Added Laplacian GI with subfunctions cat_surf_GI3D and
          cat_surf_epivolsurf.
New:      Added internal function cat_io_volctype to convert data to other
          datatypes, e.g. to save disk memory.



------------------------------------------------------------------------
r941 | gaser | 2016-05-26 11:31:32 +0200 (Thu, 26 May 2016) | 14 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
MM      cat_conf_fmri.m
MM      cat_fmri_main.m
MM      cat_fmri_multi_run.m
M       html/cat_starting.html

Changed: Updated manual.



------------------------------------------------------------------------
r940 | gaser | 2016-05-21 01:01:48 +0200 (Sat, 21 May 2016) | 9 lines

Changed paths:
M       CHANGES.txt

(1) Changed: Prepared surf2roi function with internal resampling.
(2) Changed: Updated manual (splitting of processes)
(3) Changed: Removed some redundant atlas files and renames aparc atlases.
(4) Changed: Renamed original cat_surf_surf2roi.m function into
    cat_surf_surf2roi_resampled.m (for resampled data only).

------------------------------------------------------------------------
r939 | gaser | 2016-05-21 01:01:27 +0200 (Sat, 21 May 2016) | 37 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
D       atlases_surfaces/lh.aparc.freesurfer.annot
D       atlases_surfaces/lh.aparcDKT40.freesurfer.annot
D       atlases_surfaces/lh.aparcDKT40JT.freesurfer.annot
A  +    atlases_surfaces/lh.aparc_DKT40.freesurfer.annot
A  +    atlases_surfaces/lh.aparc_DKT40JT.freesurfer.annot
R  +    atlases_surfaces/lh.aparc_a2005s.freesurfer.annot
R  +    atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
A  +    atlases_surfaces/lh.aparc_freesurfer.annot
D       atlases_surfaces/lh.rois.a2009s.txt
D       atlases_surfaces/rh.aparc.freesurfer.annot
D       atlases_surfaces/rh.aparcDKT40.freesurfer.annot
D       atlases_surfaces/rh.aparcDKT40JT.freesurfer.annot
A  +    atlases_surfaces/rh.aparc_DKT40.freesurfer.annot
A  +    atlases_surfaces/rh.aparc_DKT40JT.freesurfer.annot
R  +    atlases_surfaces/rh.aparc_a2005s.freesurfer.annot
R  +    atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
A  +    atlases_surfaces/rh.aparc_freesurfer.annot
D       atlases_surfaces/rh.rois.a2009s.txt
D       atlases_surfaces/rois.a2009s.txt
M       cat12.fig
M       cat12.m
M       cat_conf_fmri.m
M       cat_conf_stools.m
M       cat_surf_surf2roi.m
A  +    cat_surf_surf2roi_resampled.m
M       tbx_cfg_cat.m

(1) Changed: Prepared surf2roi function with internal resampling.
(2) Changed: Updated manual (splitting of processes)
(3) Changed: Removed some redundant atlas files and renames aparc atlases.
(4) Changed: Renamed original cat_surf_surf2roi.m function into
    cat_surf_surf2roi_resampled.m (for resampled data only).

------------------------------------------------------------------------
r938 | gaser | 2016-05-19 10:35:43 +0200 (Thu, 19 May 2016) | 16 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_stat_check_cov.m
MM      cat_surf_flipsides.m
M       html/cat.html
M       html/cat_starting.html

(1) Changed: Mahalanobis distance can be now displayed in cat_stat_check_cov.m
(2) Changed: Updated manual regarding homogeneity check.


------------------------------------------------------------------------
r937 | gaser | 2016-05-12 10:56:23 +0200 (Thu, 12 May 2016) | 17 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
A       cat_conf_fmri.m
M       cat_conf_tools.m
A       cat_fmri_main.m
A       cat_fmri_multi_run.m
M       cat_surf_createCS.m
M       cat_vol_groupwise_ls.m
M       html/cat.html

(1) Fixed: Error in cat_surf_createCS.m where range of temporarily saved files
    was wrong.
(2) Fixed: Error in longitudinal pipeline for masked registration.
(3) Added: Experimental code for fMRI batch.


------------------------------------------------------------------------
r936 | dahnke | 2016-05-11 17:59:17 +0200 (Wed, 11 May 2016) | 35 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_io_report.m
M       cat_main_LAS.m
M       cat_main_gintnorm.m
M       cat_run.m
M       cat_run_job.m
M       cat_surf_display.m
A       cat_surf_flipsides.m
M       cat_surf_rename.m
M       cat_surf_render.m
M       html/cat.html
M       html/cat.txt

Fixed*:   Corrected APP option to use the bias corrected image.
Fixed*:   Corrected lighting problems with CAT surface renderer under
          Windows and Linux.
Changed*: Set cat.extopts.resval parameter to avoid interpolation.
Added*:   Intensity scaling functions for cat_surf_display (cat_surf_render).
Added*:   Material and lighting options for cat_surf_display (cat_surf_render).
Added:    Added lazy processing for EXPERTs for CAT segmentation.
          This allows to avoid the preprocessing, if the same parameter are used
          and the expected results exist.
          This function is useful for problems in large datasets, if the
          preprocessing of some subjects or complete jobs failed by internal
          (small cat errors) or external (matlab or systems error, server errors).
Added:    EXPERT function and files to flip the side of the surface.
Fixed:    Some HTML help layout problems.
Fixed:    Small changes for CSF thresholds in cat_main_gintnorm and cat_main_LAS.



------------------------------------------------------------------------
r935 | gaser | 2016-05-11 14:17:58 +0200 (Wed, 11 May 2016) | 65 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_amap.mexa64
M       cat_amap.mexmaci64
M       cat_amap.mexw64
M       cat_ornlm.mexa64
M       cat_ornlm.mexmaci64
M       cat_ornlm.mexw64
M       cat_sanlm.mexa64
M       cat_sanlm.mexmaci64
M       cat_sanlm.mexw64
M       cat_surf_createCS.m
M       cat_vbdist.mexa64
M       cat_vbdist.mexmaci64
M       cat_vbdist.mexw64
M       cat_vol_downcut.mexa64
M       cat_vol_downcut.mexmaci64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.mexa64
M       cat_vol_eidist.mexmaci64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.c
M       cat_vol_genus0.mexa64
M       cat_vol_genus0.mexmaci64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.mexa64
M       cat_vol_gradient3.mexmaci64
M       cat_vol_gradient3.mexw64
M       cat_vol_groupwise_ls.m
M       cat_vol_interp3f.mexa64
M       cat_vol_interp3f.mexmaci64
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.mexa64
M       cat_vol_laplace3.mexmaci64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mexa64
M       cat_vol_laplace3R.mexmaci64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexa64
M       cat_vol_localstat.mexmaci64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexa64
M       cat_vol_median3.mexmaci64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexa64
M       cat_vol_median3c.mexmaci64
M       cat_vol_median3c.mexw64
M       cat_vol_pbtp.mexa64
M       cat_vol_pbtp.mexmaci64
M       cat_vol_pbtp.mexw64
M       cat_vol_simgrow.mexa64
M       cat_vol_simgrow.mexmaci64
M       cat_vol_simgrow.mexw64
M       compile.m
M       html/cat.html
M       internal/cat_vol_cMRegularizarNLM3Dw.c

(1) Fixed: Error in genus0.c and cat_vol_genus0.c if function fails and no
    output is returned.
(2) Changed: Added a more refined final bias correction between scans to
    longitudinal pipeline.
(3) Fixed: Some compilation issues under windows.


------------------------------------------------------------------------
r934 | gaser | 2016-04-26 11:16:32 +0200 (Tue, 26 Apr 2016) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_vol_groupwise_ls.m
M       html/cat.html
 M      templates_surfaces/lh.mc.central.freesurfer.gii
 M      templates_surfaces/rh.mc.central.freesurfer.gii

(1) Fixed: TFCE option is now disabled if toolbox is not found.
(2) Changed: Noise estimation is set to "1" for all files if one file receives
    a NaN.


------------------------------------------------------------------------
r933 | dahnke | 2016-04-25 14:58:08 +0200 (Mon, 25 Apr 2016) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat_run.m
M       cat_surf_calc.m
M       cat_surf_display.m
M       cat_surf_info.m
M       cat_surf_rename.m
M       cat_surf_render.m
M       html/cat.html
M       html/cat.txt
M       html/cat_methods.html
M       html/style.css

Fixed:    Corrected HTML style for MATLAB 2016a.
Fixed:    Corrected colormap surface display problems for MATLAB 2016a.
Fixed:    Corrected cat_surf_calc naming problem and prepared further tests.

------------------------------------------------------------------------
r932 | gaser | 2016-04-22 13:11:51 +0200 (Fri, 22 Apr 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_long_main.m
M       cat_vol_groupwise_ls.m
M       html/cat.html

Fixed: Error in longitudinal pipeline where the mask for registration was
       not correct.

------------------------------------------------------------------------
r931 | gaser | 2016-04-21 16:28:56 +0200 (Thu, 21 Apr 2016) | 23 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_stat_check_cov.m
M       cat_stat_spmF2x.m
M       cat_stat_spmT2x.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
D       cat_surf_resample.m
M       html/cat.html
A       templates_surfaces/lh.mc.central.freesurfer.gii
A       templates_surfaces/rh.mc.central.freesurfer.gii
M       templates_surfaces/templates_surfaces.man

(1) Removed: cat_surf_resample.m which is replaced by cat_surf_resamp.m.
(2) Added: Mean curvature template ?h.mc.central.freesurfer.gii.
(3) Changed: Handlinbg if fwhm=0 in cat_surf_resamp_freesurfer.m.
(4) Fixed: Crashes if cluster extent threshold was selected for some cases
    in cat_stat_spmT2x.m and cat_stat_spmF2x.m.


------------------------------------------------------------------------
r930 | gaser | 2016-04-20 11:34:52 +0200 (Wed, 20 Apr 2016) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_defaults.m
MM      cat_long_APP.m
M       cat_surf_createCS.m
M       html/cat.html

Changed: Initial intensity-based topology correction using tca set as default.


------------------------------------------------------------------------
r929 | gaser | 2016-04-19 12:10:13 +0200 (Tue, 19 Apr 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_long_APP.m
M       cat_surf_createCS.m
M       cat_vol_groupwise_ls.m

Changed: Added masked registration to longitudinal pipeline.
Changed: Initial intensity-based topology correction using tca from BrainSuite.


------------------------------------------------------------------------
r928 | dahnke | 2016-04-15 17:08:32 +0200 (Fri, 15 Apr 2016) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_long_APP.m
M       cat_main.m
M       cat_run_job.m
M       cat_version.m

Fixed:    Use CHANGES.txt for a second CAT version estimation.
Fixed:    Report colormap scaling.
Fixed:    Updated help of cat_long_APP.
Changed:  Removed old code.



------------------------------------------------------------------------
r927 | dahnke | 2016-04-15 09:32:26 +0200 (Fri, 15 Apr 2016) | 7 lines

Changed paths:
M       CHANGES.txt
A       cat_long_APP.m

New*:      APP for longitudinal pipeline.


------------------------------------------------------------------------
r926 | dahnke | 2016-04-14 16:16:11 +0200 (Thu, 14 Apr 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_run_job_APP_init.m

Fixed*:    Corrected initial APP for small (negative) values.
New*:      APP for longitudinal pipeline.


------------------------------------------------------------------------
r925 | dahnke | 2016-04-13 17:52:20 +0200 (Wed, 13 Apr 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_io_writenii.m

Fixed:    Corrected writing of rigid and affine output.

------------------------------------------------------------------------
r924 | dahnke | 2016-04-13 17:38:28 +0200 (Wed, 13 Apr 2016) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_io_writenii.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_run.m

Fixed:    Corrected small error and warnings unter Windows and Linux.


------------------------------------------------------------------------
r923 | dahnke | 2016-04-13 15:35:13 +0200 (Wed, 13 Apr 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_run_job.m

Fixed:    Corrected small errors by wrong data-type due to noise-correction.

------------------------------------------------------------------------
r922 | dahnke | 2016-04-13 14:37:56 +0200 (Wed, 13 Apr 2016) | 27 lines

Changed paths:
M       CHANGES.txt
M       cat_io_report.m
M       cat_io_writenii.m
M       cat_io_xml.m
M       cat_main.m
M       cat_main_cleanup.m
M       cat_main_gcut.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job_APP_init.m
M       cat_stat_check_cov.m
M       cat_tst_calc_kappa.m
M       cat_vol_partvol.m

Fixed*:    Corrected APP1 WMth estimation error for low value longitudinal data.
Fixed*:    Corrected problems with to strong WMHC in images with low resolution,
           high noise and increase neutral zone around the basal ganglia.
Fixed:     Skull-striping warnings in low resolution images.
Fixed:     Corrected error in GUI resolution variable.
Fixed:     Corrected error in cat_io_xml.
Fixed:     Deactivated spm_DATE.ps output in case of error.
Changed*:  Updated cleanup Function.
Changed*:  Added initial noise correction.
Changed:   Added possible output variable to cat_stat_check_cov.
Changed:   Modified brain mask threshold to include CSF in cat_tst_calc_kappa.

------------------------------------------------------------------------
r921 | dahnke | 2016-04-08 16:57:33 +0200 (Fri, 08 Apr 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_display_matlab_PID.m

Fixed:    Corrected PID display function.

------------------------------------------------------------------------
r920 | gaser | 2016-04-08 16:24:27 +0200 (Fri, 08 Apr 2016) | 10 lines

Changed paths:
M       CHANGES.txt
MM      cat_display_matlab_PID.m
M       cat_surf_calc.m
 M      internal/cat_tst_BWPres.m
MM      internal/cat_vol_reduceRes.m

Fixed: Issue in cat_stat_surf. Thanks to Christoph Hofstetter for pointing
       to that issue.

------------------------------------------------------------------------
r919 | gaser | 2016-04-08 12:38:28 +0200 (Fri, 08 Apr 2016) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_stat_spmT2x.m
M       html/cat.html

Changed: Corrected some typos and changed help text.

------------------------------------------------------------------------
r918 | dahnke | 2016-04-07 19:20:56 +0200 (Thu, 07 Apr 2016) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_LAS.m
M       cat_main_gcut.m

Fixed:    Corrected Yms error.
Fixed:    Corrected further problems of LAS in large ventricles.
Changed:  Less agressive skull-stripping.
Changed:  More CSF in skull-stripping.
Changed:  Cleanup only for voxel <1.9.



------------------------------------------------------------------------
r917 | dahnke | 2016-04-05 17:43:37 +0200 (Tue, 05 Apr 2016) | 31 lines

Changed paths:
M       CHANGES.txt
A       cat_display_matlab_PID.m
M       cat_io_writenii.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_main_gintnorm.m
M       cat_parallelize.m
M       cat_run.m
M       cat_surf_calc.m
M       cat_surf_info.m
M       cat_surf_resample.m
M       cat_surf_surf2roi.m
M       cat_vol_isarnlm.m
M       cat_vol_sanlm.m
 M      internal
A       internal/cat_tst_BWPres.m
M       internal/cat_vol_nlmus.m
A       internal/cat_vol_reduceRes.m
 M      templates_1.50mm

Fixed:    Corrected error for undefined job.nprog of GUI without nprog parameter.
Fixed:    Peak estimation problem in subjects with very large ventricle.
Fixed:    Further problems of LAS for large ventricle.
Changed:  Removed Peak-Waring.






------------------------------------------------------------------------
r916 | gaser | 2016-04-04 15:27:19 +0200 (Mon, 04 Apr 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       html/cat.html
M       spm_cat12.m

Fixed: Error in spm_cat12 that gives wrong warnig about not compatible
       binaries for surface processing.


------------------------------------------------------------------------
r915 | gaser | 2016-03-30 15:57:12 +0200 (Wed, 30 Mar 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_run.m
M       cat_surf_resamp.m
M       html/cat.html

Fixed: Issue with cat_surf_resamp in parallel mode with same filenames


------------------------------------------------------------------------
r914 | gaser | 2016-03-29 02:46:29 +0200 (Tue, 29 Mar 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_system.m
M       html/cat.html

Fixed: Issue with cat_system (hopefully).


------------------------------------------------------------------------
r913 | gaser | 2016-03-29 02:17:14 +0200 (Tue, 29 Mar 2016) | 20 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_io_FreeSurfer.m
M       cat_stat_spmT2x.m
M       cat_surf_avg.m
M       cat_surf_calc.m
M       cat_surf_createCS.m
M       cat_surf_parameters.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
M       cat_surf_resample.m
M       cat_surf_smooth.m
M       cat_surf_vol2surf.m
M       cat_system.m
M       html/cat.html

Fixed: Issue with cat_system (hopefully).


------------------------------------------------------------------------
r912 | gaser | 2016-03-22 23:54:01 +0100 (Tue, 22 Mar 2016) | 23 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_io_senderrormail.m
M       cat_main.m
M       cat_parallelize.m
M       cat_surf_avg.m
M       cat_surf_createCS.m
M       cat_surf_parameters.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
M       cat_surf_smooth.m
M       cat_surf_vol2surf.m
M       html/cat.html

(1) Fixed: Issue with sendmail under windows.
(2) Changed: Replaced cat_system with system because of errors under
    windows.
(3) Changed: Commented out try and catch part for surface creation in
    cat_main.m because no real error messages can be obtained.
(4) Fixed: System calls are now made in the folder of the binaries to
    prevent issues with spaces in filenames and folders under windows.

------------------------------------------------------------------------
r911 | gaser | 2016-03-21 17:26:16 +0100 (Mon, 21 Mar 2016) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
MM      atlases_surfaces/a2005s.txt
MM      atlases_surfaces/a2009s.txt
MM      atlases_surfaces/dkt40.txt
MM      atlases_surfaces/pals.txt
M       html/cat.html
M       html/cat.txt
M       html/cat_tools_SBM.html
M       html/cat_tools_VBM.html
M       templates_surfaces/templates_surfaces.man

Changed: Some updates to html-code.

------------------------------------------------------------------------
r910 | gaser | 2016-03-21 15:56:55 +0100 (Mon, 21 Mar 2016) | 6 lines

Changed paths:
M       CHANGES.txt

Changed: Surface atlases are now in a separate folder atlases_surfaces
Added: Info files for Freesurfer atlases.

------------------------------------------------------------------------
r909 | gaser | 2016-03-21 15:56:45 +0100 (Mon, 21 Mar 2016) | 87 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
A       atlases_surfaces
A       atlases_surfaces/a2005s.txt
A       atlases_surfaces/a2009s.txt
A       atlases_surfaces/dkt40.txt
A  +    atlases_surfaces/lh.PALS_B12_Brodmann.freesurfer.annot
A  +    atlases_surfaces/lh.PALS_B12_Lobes.freesurfer.annot
A  +    atlases_surfaces/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
A  +    atlases_surfaces/lh.PALS_B12_Visuotopic.freesurfer.annot
A  +    atlases_surfaces/lh.aal.Template_T1_IXI555_MNI152
A  +    atlases_surfaces/lh.aparc.freesurfer.annot
A  +    atlases_surfaces/lh.aparcDKT40.freesurfer.annot
A  +    atlases_surfaces/lh.aparcDKT40JT.freesurfer.annot
A  +    atlases_surfaces/lh.aparc_a2005s.freesurfer.annot
A  +    atlases_surfaces/lh.aparc_a2009s.freesurfer.annot
A  +    atlases_surfaces/lh.hammers.Template_T1_IXI555_MNI152
A  +    atlases_surfaces/lh.lpba40.Template_T1_IXI555_MNI152
A  +    atlases_surfaces/lh.mori.Template_T1_IXI555_MNI152
A  +    atlases_surfaces/lh.neuromorphometrics.Template_T1_IXI555_MNI152
A  +    atlases_surfaces/lh.rois.a2009s.txt
A       atlases_surfaces/pals.txt
A  +    atlases_surfaces/rh.PALS_B12_Brodmann.freesurfer.annot
A  +    atlases_surfaces/rh.PALS_B12_Lobes.freesurfer.annot
A  +    atlases_surfaces/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
A  +    atlases_surfaces/rh.PALS_B12_Visuotopic.freesurfer.annot
A  +    atlases_surfaces/rh.aal.Template_T1_IXI555_MNI152
A  +    atlases_surfaces/rh.aparc.freesurfer.annot
A  +    atlases_surfaces/rh.aparcDKT40.freesurfer.annot
A  +    atlases_surfaces/rh.aparcDKT40JT.freesurfer.annot
A  +    atlases_surfaces/rh.aparc_a2005s.freesurfer.annot
A  +    atlases_surfaces/rh.aparc_a2009s.freesurfer.annot
A  +    atlases_surfaces/rh.hammers.Template_T1_IXI555_MNI152
A  +    atlases_surfaces/rh.lpba40.Template_T1_IXI555_MNI152
A  +    atlases_surfaces/rh.mori.Template_T1_IXI555_MNI152
A  +    atlases_surfaces/rh.neuromorphometrics.Template_T1_IXI555_MNI152
A  +    atlases_surfaces/rh.rois.a2009s.txt
A  +    atlases_surfaces/rois.a2009s.txt
M       cat_roi_roi2surf.m
M       cat_surf_surf2roi.m
M       html/cat.html
M       html/cat.txt
M       html/cat_methods_RBM.html
M       templates_1.50mm/aal.txt
M       templates_1.50mm/anatomy.txt
M       templates_1.50mm/hammers.txt
M       templates_1.50mm/ibsr.txt
M       templates_1.50mm/lpba40.txt
M       templates_1.50mm/mori.txt
D       templates_surfaces/lh.PALS_B12_Brodmann.freesurfer.annot
D       templates_surfaces/lh.PALS_B12_Lobes.freesurfer.annot
D       templates_surfaces/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
D       templates_surfaces/lh.PALS_B12_Visuotopic.freesurfer.annot
D       templates_surfaces/lh.aal.Template_T1_IXI555_MNI152
D       templates_surfaces/lh.aparc.freesurfer.annot
D       templates_surfaces/lh.aparcDKT40.freesurfer.annot
D       templates_surfaces/lh.aparcDKT40JT.freesurfer.annot
D       templates_surfaces/lh.aparc_a2005s.freesurfer.annot
D       templates_surfaces/lh.aparc_a2009s.freesurfer.annot
D       templates_surfaces/lh.hammers.Template_T1_IXI555_MNI152
D       templates_surfaces/lh.lpba40.Template_T1_IXI555_MNI152
D       templates_surfaces/lh.mori.Template_T1_IXI555_MNI152
D       templates_surfaces/lh.neuromorphometrics.Template_T1_IXI555_MNI152
D       templates_surfaces/lh.rois.a2009s.txt
D       templates_surfaces/rh.PALS_B12_Brodmann.freesurfer.annot
D       templates_surfaces/rh.PALS_B12_Lobes.freesurfer.annot
D       templates_surfaces/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
D       templates_surfaces/rh.PALS_B12_Visuotopic.freesurfer.annot
D       templates_surfaces/rh.aal.Template_T1_IXI555_MNI152
D       templates_surfaces/rh.aparc.freesurfer.annot
D       templates_surfaces/rh.aparcDKT40.freesurfer.annot
D       templates_surfaces/rh.aparcDKT40JT.freesurfer.annot
D       templates_surfaces/rh.aparc_a2005s.freesurfer.annot
D       templates_surfaces/rh.aparc_a2009s.freesurfer.annot
D       templates_surfaces/rh.hammers.Template_T1_IXI555_MNI152
D       templates_surfaces/rh.lpba40.Template_T1_IXI555_MNI152
D       templates_surfaces/rh.mori.Template_T1_IXI555_MNI152
D       templates_surfaces/rh.neuromorphometrics.Template_T1_IXI555_MNI152
D       templates_surfaces/rh.rois.a2009s.txt
D       templates_surfaces/rois.a2009s.txt
M       templates_surfaces/templates_surfaces.man

Changed: Surface atlases are now in a separate folder atlases_surfaces
Added: Info files for Freesurfer atlases.

------------------------------------------------------------------------
r908 | gaser | 2016-03-21 13:01:27 +0100 (Mon, 21 Mar 2016) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       html/cat.html
M       html/cat_FAQ.html
M       html/cat_ackknowledgement.html
M       html/cat_methods_QA.html
M       html/cat_methods_RBM.html
M       html/cat_tools_ROI.html
M       html/cat_tools_SBM.html
M       html/cat_tools_VBM.html

Changed: Updated html code.

------------------------------------------------------------------------
r907 | gaser | 2016-03-21 10:20:04 +0100 (Mon, 21 Mar 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_vol_sanlm.m

Changed: Increased filter strength for adaptive NLM-filtering.

------------------------------------------------------------------------
r906 | dahnke | 2016-03-18 18:23:10 +0100 (Fri, 18 Mar 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_LAS.m
M       cat_parallelize.m
M       cat_vol_isarnlm.m
M       cat_vol_sanlm.m

Fixed:  Problems with sanlm filter strength.

------------------------------------------------------------------------
r905 | gaser | 2016-03-18 16:34:50 +0100 (Fri, 18 Mar 2016) | 18 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat12.fig
M       cat12.m
M       cat_io_senderrormail.m
M       html/cat.html
M       html/cat.txt
M       html/cat_methods_QA.html
M       html/cat_methods_VBM.html

Changed: Updated html text.
Changed: Updated manual.
Changed: Added "Send Error" button to GUI.


------------------------------------------------------------------------
r904 | dahnke | 2016-03-18 13:50:19 +0100 (Fri, 18 Mar 2016) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_io_report.m
MM      cat_io_senderrormail.m
M       cat_main.m
M       cat_vol_isarnlm.m
M       cat_vol_sanlm.m
 M      html/cat_methods_caterrorreporthelp.html
 M      html/cat_methods_catreporthelp.html

Changed:  Refined noise estimation in cat_vol_sanlm and cat_main.
Added:    Verbose output in cat_vol_sanlm.
Fixed:    Error in error report generation.

------------------------------------------------------------------------
r903 | dahnke | 2016-03-17 19:10:34 +0100 (Thu, 17 Mar 2016) | 22 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
M       cat_main_gintnorm.m
M       cat_parallelize.m
M       cat_run.m
M       cat_run_job.m
M       cat_vol_isarnlm.m
M       cat_vol_sanlm.m
M       internal/cat_vol_nlmus.m

Added*:   Update SANLM filter with a (automatic) global strength parameter.
Fixed*:   Corrected error in gintnorm for small values.
Fixed:    Corrected rounding error in nlmus.
Fixed:    Corrected background problem if msk field is used in the SPM
          preprocessing.
Added:    Parallel output of Ym class maps pi#*.nii in developer mode (expertgui>1)
Added:    Output of PID in parallel processing to kill zombies.


------------------------------------------------------------------------
r902 | dahnke | 2016-03-14 18:04:09 +0100 (Mon, 14 Mar 2016) | 18 lines

Changed paths:
M       CHANGES.txt
A       cat_io_senderrormail.m
M       cat_io_xml.m
M       cat_run_newcatch.m
M       cat_surf_calc.m
A       html/cat_methods_caterrorreporthelp.html
A       html/cat_methods_catreporthelp.html
M       html/style.css

Added:    Added function to send error messages (cat_io_senderrormail) that
          open a new email with the mailto function with standard text with
          system and error information.
          Does not work under Linux were the error message is just printed as
          webpage in the browser.
Fixed:    Corrected some small errors.


------------------------------------------------------------------------
r901 | gaser | 2016-03-14 16:51:57 +0100 (Mon, 14 Mar 2016) | 18 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_surf_render.m
M       cat_surf_resamp.m
M       cat_surf_vol2surf.m
M       html/cat.html

Fixed: Doubled gii.gii extension in cat_surf_vol2surf.m
Fixed: Wrong gii-extension after resampling, should be freesurfer format.
Fixed: Slider option is added after overlay in cat_surf_render.m.
Fixed: Surface mapping for WM/CSF is not yet wiorking, moved to exp-mode 2.
Fixed: Underlying surface after cat12-call (estimate) was not correct.


------------------------------------------------------------------------
r900 | gaser | 2016-03-13 17:06:13 +0100 (Sun, 13 Mar 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
MM      cat_system.m
M       cat_update.m
M       html/cat.html

Fixed: Wrong update function.


------------------------------------------------------------------------
r899 | gaser | 2016-03-13 16:51:12 +0100 (Sun, 13 Mar 2016) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_update.m
M       html/cat.html
 M      html/images/CAT_Error_Report.jpg
 M      html/images/CAT_Report.jpg

Fixed: Wrong update function.


------------------------------------------------------------------------
r898 | gaser | 2016-03-13 16:44:00 +0100 (Sun, 13 Mar 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
A       cat_system.m
M       html/cat.html

Fixed: Added missing cat_system.m


------------------------------------------------------------------------
r897 | dahnke | 2016-03-11 18:06:26 +0100 (Fri, 11 Mar 2016) | 20 lines

Changed paths:
M       CHANGES.txt
M       cat_io_report.m
M       cat_io_xml.m
M       cat_main.m
M       cat_main_gcut.m
M       cat_vol_partvol.m
M       html/cat_methods_errormanagement.html
M       html/cat_tools_ROI.html
A       html/images/CAT_Error_Report.jpg
A       html/images/CAT_Report.jpg

Fixed:    Corrected initial skull-stripping problem in large ventricle subjects.
Fixed:    Sign error to choose skull-stripping for T2/PD processing.
Fixed:    Corrected display error for long filenames in cat_io_xml.
Changed:  Updated CAT error report.
Added:    First version of error mail report.



------------------------------------------------------------------------
r896 | gaser | 2016-03-11 17:27:05 +0100 (Fri, 11 Mar 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_run.m
M       html/cat.html

Fixed: Added toolbox folders to addpath in cat_main.m again.


------------------------------------------------------------------------
r895 | gaser | 2016-03-11 17:07:09 +0100 (Fri, 11 Mar 2016) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults_expert.m
M       cat_parallelize.m
M       cat_run.m
M       cat_surf_createCS.m
M       cat_surf_display.m
M       spm_cat12.m

(1) Fixed: Issues with spaces in folder names under windows.
(2) Changed: Some typos.


------------------------------------------------------------------------
r894 | dahnke | 2016-03-10 14:50:04 +0100 (Thu, 10 Mar 2016) | 23 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
MM      cat_defaults_expert.m
MM      cat_io_report.m
M       cat_main.m
M       cat_main_LAS.m
MM      cat_roi_roi2surf.m
M       cat_run_job.m
M       cat_run_newcatch.m
M       cat_run_oldcatch.m
M       cat_vol_isarnlm.m
 M      html/images/CAT_surf_atlas_Destrieux.png
MM      internal/cat_vol_increaseAtlasGMregion.m

Changed:    Updated CAT error report, improved image display, histogram range
            and added a global error variable to print basic SPM parameter
            created in the preprocessing.
Fixed*:     Corrected problems in LAS processing.




------------------------------------------------------------------------
r893 | gaser | 2016-03-10 09:49:52 +0100 (Thu, 10 Mar 2016) | 13 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       html/cat.html
M       html/cat_methods_RBM.html
M       html/cat_methods_VBM.html

(1) Fixed: Some typos in html code.
(2) Changed: Updated manual.


------------------------------------------------------------------------
r892 | dahnke | 2016-03-09 18:57:21 +0100 (Wed, 09 Mar 2016) | 25 lines

Changed paths:
 M      .
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_defaults.m
A       cat_defaults_expert.m
M       cat_io_report.m
M       cat_main.m
A       cat_roi_roi2surf.m
M       cat_surf_createCS.m
M       cat_surf_display.m
M       cat_surf_info.m
M       cat_vol_isarnlm.m
M       spm_cat12.m
M       tbx_cfg_cat.m

Fixed:    Correction NaN thickness error in CAT report.
Added:    New expert function to project ROI data from XML and CSV files to the
          surface (cat_surf_roi2surf).
Added:    cat_defaults_expert.m for GUI and processing tests such as
          surface and ROI processing with ignoreErrors=1.




------------------------------------------------------------------------
r891 | dahnke | 2016-03-09 11:39:00 +0100 (Wed, 09 Mar 2016) | 29 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_stools.m
M       cat_io_colormaps.m
M       cat_io_csv.m
A       cat_io_report.m
M       cat_main.m
M       cat_run_newcatch.m
M       cat_run_oldcatch.m
M       cat_vol_isarnlm.m
M       html/cat_methods_QA.html
M       html/cat_methods_RBM.html
M       html/cat_methods_defaults.html
M       html/cat_methods_errormanagement.html
A       html/images/CAT_surf_atlas_Destrieux.png
A       internal/cat_vol_increaseAtlasGMregion.m
M       templates_1.50mm/neuromorphometrics.nii

Fixed*:   Corrected problems in the processing of T2/PD data.
Fixed:    Corrected neuromorphometrics atlas for lower GM probability threshold.
Fixed:    Corrected variable error in the ROI processing.
Changed:  Visuell update of the CAT Report colormap that the indicated colors
          fits better to the defined tissues.
Changed:  Update of some HTML help pages.
Added:    Small internal function for the neuromorphometrics optimization.
Added:    Prepared first version of CAT error export.


------------------------------------------------------------------------
r890 | gaser | 2016-03-08 15:43:19 +0100 (Tue, 08 Mar 2016) | 15 lines

Changed paths:
M       Amap.c
M       CHANGES.txt
M       Contents.m
M       Kmeans.c
M       cat_amap.mexa64
M       cat_amap.mexmaci64
M       cat_run.m
M       cat_update.m
M       html/cat.html

(1) Changed: Update function to solve some issues.
(2) Fixed: Nasty java error by not using "\b" in c-files anymore.
(3) Fixed: Issue with longitzudinal batch.

------------------------------------------------------------------------
r889 | gaser | 2016-03-07 17:01:59 +0100 (Mon, 07 Mar 2016) | 14 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_main.m
M       html/cat.html
M       html/cat_methods_RBM.html
M       spm_cat12.m

(1) Changed: Updated manual.
(2) Fixed: Some typos.

------------------------------------------------------------------------
r888 | dahnke | 2016-03-07 11:01:12 +0100 (Mon, 07 Mar 2016) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_io_cprintf.m
M       cat_parallelize.m
M       cat_run.m
 M      html/cat_methods_defaults.html
 M      html/cat_methods_errormanagement.html
M       spm_cat12.m

Fixed:    Corrected error by cprintferror in parallel processing.

------------------------------------------------------------------------
r887 | dahnke | 2016-03-07 08:57:04 +0100 (Mon, 07 Mar 2016) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_io_cgw2seg.m
M       cat_io_cprintf.m
M       cat_main.m
M       cat_parallelize.m
M       cat_run.m
M       cat_run_job.m
M       html/cat_methods_RBM.html
M       spm_cat12.m

Changed:    Use affine aligned image in CAT report.

------------------------------------------------------------------------
r886 | gaser | 2016-03-04 16:36:03 +0100 (Fri, 04 Mar 2016) | 15 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_run_job.m
M       cat_run_job_APP_init.m
M       tbx_cfg_cat.m

(1) Changed: Updated manual.
(2) Changed: Changed some help text.
(3) Fixed: Some out of range errors and divs by zeros
(4) Changed: Default NCstr is now 0.75

------------------------------------------------------------------------
r885 | dahnke | 2016-03-04 16:11:00 +0100 (Fri, 04 Mar 2016) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_run_job.m
M       html/cat.html
M       html/cat.txt
M       html/cat_methods.html
M       html/cat_methods_VBM.html
A       html/cat_methods_defaults.html
A       html/cat_methods_errormanagement.html
M       html/style.css

Changed:    Use only default parameter for initial affine registration.
Added:      Wrote error-management help.
Added       Wrote cat_defaults and user-modes help.

------------------------------------------------------------------------
r884 | gaser | 2016-03-04 12:11:12 +0100 (Fri, 04 Mar 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_surf_display.m
M       cat_surf_render.m

(1) Fixed: Wrong weighting of NCstr in cat_main.m
(2) Changed: Use try for call of cat_surf_display and cat_surf_render because of
    weird error in Matlkab 2015a with non-double values for Faces.

------------------------------------------------------------------------
r883 | dahnke | 2016-03-04 12:00:18 +0100 (Fri, 04 Mar 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_tst_qa.m

Fixed:    Corrected error in CAT.XML due to the usage of cat_get_defaults rather
          than using the job structure.
Fixed:    Corrected wrong use of job.extopts.NCstr parameter in cat_main.
Changed:  Memory optimization of SPM preprocessing.

------------------------------------------------------------------------
r882 | dahnke | 2016-03-03 18:14:22 +0100 (Thu, 03 Mar 2016) | 25 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_main_gintnorm.m
M       cat_run_job.m
M       cat_run_newcatch.m
M       cat_run_oldcatch.m
M       cat_tst_qa.m
M       html/cat_methods.html
M       html/cat_methods_VBM.html

Changed*:   Further test of the affine registration for untypical scaling and
            switching to the default registration option that seems to be more
            robust.
            *** This part is experimental and required further work and tests!
Fixed:      Corrected error in cat_main line 1920 - missed variable hhm.
Fixed:      Corrected error in cat_tst_qa line 646 - interpolation error due to
            bad V.pinfo field.
Fixed:      Corrected error due to bad background estimation in cat_main line 411.
Changed:    Added an error message if SPM Segmentation is empty.
Changed:    Used error identifier rather that error message for the name of the
            error subdirectory created in the catch block in cat_run_[new|old]catch
Changed:    Updated contrast checks and error message in cat_main_gintnorm.


------------------------------------------------------------------------
r881 | gaser | 2016-03-03 11:41:28 +0100 (Thu, 03 Mar 2016) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       cat_surf_parameters.m
M       html/cat.html
M       html/cat.txt

(1) Changed: mrf filter is now independent from NCstr and is limited to <=0.15
(2) Fixed: Issue with old use of log rather than sqrt for slucus depth
    estimation
(3) Fixed: Browser commands in cat.txt

------------------------------------------------------------------------
r880 | dahnke | 2016-03-02 20:06:35 +0100 (Wed, 02 Mar 2016) | 18 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_main.m
M       cat_run_job.m
M       cat_stat_marks.m
M       html/cat.html
M       html/cat.txt
M       html/cat_methods_LP.html
M       html/cat_methods_MS.html
M       html/cat_methods_VBM.html

Fixed:      Removed incorrect error message in cat_run_job
Fixed:      Corrected quality grading function for NaN input.
Changed:    Replaced QA marks with percentage rating and grade in command line report.
Changed:    Updated HTML help.


------------------------------------------------------------------------
r879 | dahnke | 2016-03-02 14:02:55 +0100 (Wed, 02 Mar 2016) | 22 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_run_job.m
D       html/cat_methods_CAT.html
M       html/cat_methods_LP.html
M       html/cat_methods_VBM.html
M       html/cat_methods_VBM_APP.html
M       html/cat_starting.html
M       html/cat_tools_VBM.html
M       html/style.css
M       spm_cat12.m
 M      templates_surfaces/lh.mask
 M      templates_surfaces/rh.mask

Changed:   Updated APP GUI and help.
Changed:   Updated noise help.
Fixed:     Corrected user specific GUI initialization problems.
Fixed:     Corrected problem with analyze input images.



------------------------------------------------------------------------
r878 | dahnke | 2016-03-01 17:36:37 +0100 (Tue, 01 Mar 2016) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
M       cat_run_job.m
M       spm_cat12.m
 M      templates_1.50mm

Changed*:   Readded subvariables to control APP.
Changed:    Set default NCstr=0.5.
Corrected: 	Corrected problems do to variable name changes from cat12 to cat.
Corrected:  Small errors.


------------------------------------------------------------------------
r877 | gaser | 2016-03-01 17:08:30 +0100 (Tue, 01 Mar 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_parallelize.m
M       cat_run.m

Changed: Some minor issue swith windows and backgorund processes.

------------------------------------------------------------------------
r876 | gaser | 2016-03-01 16:39:22 +0100 (Tue, 01 Mar 2016) | 26 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_parallelize.m
M       cat_run.m
M       cat_surf_parameters.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
M       cat_surf_resample.m
M       cat_surf_smooth.m
M       cat_surf_surf2roi.m
M       html/cat.txt
M       html/cat_tools_ROI.html
M       tbx_cfg_cat.m
A       templates_surfaces/lh.mask
D       templates_surfaces/lh.mask.txt
A       templates_surfaces/rh.mask
D       templates_surfaces/rh.mask.txt

(1) Fixed: wrong parameter nprog instead of nproc in several files.
(2) Fixed: Many issues with Matlab 2015 and Windows.
(3) Changed: Use only half of cores under windows because of poor memory
    management.
(4) Changed: Some typos and wrong links in html code
(5) Fixed: Issue with *.mask.txt that was not readable under windows.

------------------------------------------------------------------------
r875 | dahnke | 2016-02-29 18:55:44 +0100 (Mon, 29 Feb 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_run_job.m

Corrected: 	Removed small error in cat_main.


------------------------------------------------------------------------
r874 | dahnke | 2016-02-29 17:01:20 +0100 (Mon, 29 Feb 2016) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_vol_isarnlm.m

Changed:    Removed old skull-striping that was applied if gcut was off.
            gcut=0 will do no skull-stripping and can be used for already
            stripped data.
            The filter is only applied within the brain mask!
Changed:    Removed old code in cat_main.
Corrected:  Error that avoid noise correction at all.
Corrected:  Small update of filter limits in cat_vol_isarnlm.

------------------------------------------------------------------------
r873 | gaser | 2016-02-29 15:29:10 +0100 (Mon, 29 Feb 2016) | 23 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_batch_long.m
M       cat_conf_extopts.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_io_FreeSurfer.m
M       cat_main.m
M       cat_plot_boxplot.m
M       cat_plot_circular.m
M       cat_stat_check_cov.m
M       cat_stat_showslice_all.m
M       cat_stat_spmF2x.m
M       cat_stat_spmT2x.m
M       cat_surf_render.m
M       cat_vol_calc_roi.m
M       cat_vol_defs.m
M       cat_vol_findfiles.m

(1) Fixed: Use of iters_icm with regard to mrf.
(2) Fixed: Some typos and code analyzer suggestions.

------------------------------------------------------------------------
r872 | dahnke | 2016-02-26 17:39:14 +0100 (Fri, 26 Feb 2016) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_main_gcut.m

Corrected:   Solved LAS problems for images with low intensity CSF range.
Corrected:   Increased closing area of gcut.
Changed:     Removed cat.extopts.print.
Changed:     Added further background variables to expert GUI.

------------------------------------------------------------------------
r871 | dahnke | 2016-02-25 16:45:42 +0100 (Thu, 25 Feb 2016) | 28 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_main.m
 M      cat_main_cleanup.m
M       cat_main_gcut.m
MM      cat_main_gcut_DEV.m
M       cat_run.m
M       cat_run_job.m

Changed*:   Updated gcut procedure.
Changed*:   Temporary inactivated initial SANLM noise correction, because SPM
            seamed to be more stable with noisier images.
Changed*:   Removed ORNLM noise correction.
Changed*:   Updated extopts.sanlm parameter:
              0 .. no denoising
              1 .. SANLM denoising (default)
              2 .. ISARNLM denoising
Changed*:   Used extopts.NCstr to weighted also the noise correction and set
            it to 0.8 because 0.5 (halt power than usual) looks to noise.
Changed*:   Added ISARNLM filter in cat_main as third option besides
            no-denoising and SANLM denoising.

              ATTENTION: Denoising is only applied within the brain mask yet!

Changed:    Corrected extopts.restypes initialization in cat_run.

------------------------------------------------------------------------
r870 | dahnke | 2016-02-24 20:39:12 +0100 (Wed, 24 Feb 2016) | 32 lines

Changed paths:
 M      .
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_main.m
A       cat_main_cleanup.m
M       cat_main_gcut.m
A       cat_main_gcut_DEV.m
M       cat_parallelize.m
M       cat_plot_boxplot.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_job_APP_final.m
M       html/cat_methods_VBM_APP.html
M       spm_cat12.m
M       tbx_cfg_cat.m

Changed*:   Added development-version of GCUT with parameter and smoothing
            update that increase impact of gcutstr.
Changed*:   Update APP control variable:
              APP0 - no APP, default preprocessing
              APP1 - light bias correction only for registration
              APP2 - light bias correction
              APP3 - fine bias correction
              APP4 - fine bias correction, skull-stripping, no affreg (primates)
Changed:    Outsourced cat_main_cleanup.
Corrected:  Small GUI call errors.
Corrected:  Reseted job.extopts.restypes in cat_run_job to get expert GUI variable.
Corrected:  Passing of a complete job variable in parallel processing.

------------------------------------------------------------------------
r869 | gaser | 2016-02-23 14:09:03 +0100 (Tue, 23 Feb 2016) | 9 lines

Changed paths:
M       Amap.c
M       CHANGES.txt
M       Contents.m
M       cat_main_gintnorm.m
M       tbx_cfg_cat.m

Fixed: Some smaller bugs from last release...

------------------------------------------------------------------------
r868 | dahnke | 2016-02-22 11:31:48 +0100 (Mon, 22 Feb 2016) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_opts.m
M       cat_main_LAS.m
M       cat_main_gintnorm.m
M       cat_run_job.m
M       cat_run_job_APP_final.m
M       cat_run_job_APP_init.m
M       tbx_cfg_cat.m

Corrected*:  Corrected atlas variable in LAS function.
Corrected:   Moved rounding help function from cat_run_job to cat_run_job_APP*.
Changed:     Added inactivated opts parameter GUI fields to expert GUI.
Changed:     Updated cat_main_gintnorm error message.


------------------------------------------------------------------------
r867 | gaser | 2016-02-20 01:03:08 +0100 (Sat, 20 Feb 2016) | 24 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_long_main.m
M       cat_run_job.m
MM      cat_run_job_APP_final.m
MM      cat_run_job_APP_init.m
 M      html/cat_methods_catreport.html
 M      html/cat_tools_VBM.html
 M      html/images/background_biasreal.png
 M      html/images/background_morphops.png
 M      html/images/background_noise.png
 M      html/images/cat_extract_addition_surface_parameter.png
 M      html/images/cat_vol_correct_slice_scaling_768.png
 M      html/images/catreport_Collins.jpg
 M      html/images/preprocessing.png

(1) Fixed: Updated manual where still the old modulation was mentioned.
(2) Fixed: @Robert: Did you really tested your last version that crashed
    because restype/resval was not correctly handled?
(3) Fixed: Issue in longitudinal batch that caused stopping after inital
    registration.

------------------------------------------------------------------------
r866 | dahnke | 2016-02-19 17:36:45 +0100 (Fri, 19 Feb 2016) | 31 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_conf_extopts.m
M       cat_defaults.m
M       cat_get_defaults.m
M       cat_io_updateStruct.m
M       cat_io_writenii.m
M       cat_main.m
M       cat_main_LAS.m
M       cat_run.m
M       cat_run_job.m
A       cat_run_job_APP_final.m
A       cat_run_job_APP_init.m
M       cat_run_newcatch.m
M       cat_run_oldcatch.m
M       cat_surf_parameters.m
M       cat_vol_partvol.m
M       html/cat_methods_VBM_APP.html
A       html/images/cat_vol_correct_slice_scaling_768.png
M       internal/cat_vol_nlmus.m
M       tbx_cfg_cat.m
A  +    templates_1.50mm/cat.nii
D       templates_1.50mm/cat12.nii

Changed*:    Major changes of the CAT parameter handling in the segmentation
             function cat_run, cat_run_job and cat_main.
             Bundle all parameters in the job variable.
Changed:     Added some help comments.
Changed:     Outsourced APP functions.

------------------------------------------------------------------------
r865 | dahnke | 2016-02-18 16:18:22 +0100 (Thu, 18 Feb 2016) | 99 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_main.m
M       cat_stat_marks.m
M       cat_vol_sanlm.m
 M      html
D       html/CAT.png
D       html/CAT_surf_atlas_DKT40.png
D       html/CAT_surf_atlas_Desikan-Killiany.png
D       html/CAT_surf_atlas_PALS-B12-Brodmann.png
D       html/CAT_surf_atlas_PALS-B12-Lobes.png
D       html/CAT_surf_atlas_aal.png
D       html/CAT_surf_atlas_hammers.png
D       html/CAT_surf_atlas_lpba40.png
D       html/CAT_surf_atlas_mori.png
D       html/CAT_surf_atlas_neuromorphometics.png
D       html/analyse_methods.png
M       html/cat.html
M       html/cat.txt
M       html/cat_FAQ.html
M       html/cat_instruction_templates.html
M       html/cat_introduction.html
M       html/cat_methods.html
M       html/cat_methods_CAT.html
M       html/cat_methods_FN.html
M       html/cat_methods_LP.html
M       html/cat_methods_MS.html
M       html/cat_methods_QA.html
M       html/cat_methods_RBM.html
M       html/cat_methods_SBM.html
M       html/cat_methods_VBM.html
A  +    html/cat_methods_VBM_APP.html
A       html/cat_methods_catreport.html
M       html/cat_methods_templates.html
D       html/cat_qa_expert.png
D       html/cat_qa_rating-distribution.png
D       html/cat_qa_rating-table.jpg
M       html/cat_starting.html
M       html/cat_stuff.html
M       html/cat_tools.html
M       html/cat_tools_FF.html
M       html/cat_tools_ROI.html
M       html/cat_tools_SBM.html
M       html/cat_tools_VBM.html
D       html/contact.jpg
D       html/cortical_measures.png
D       html/gyrification_index.png
D       html/home.jpg
D       html/human_brain.en.jpg
D       html/human_brain.png
A       html/images
A  +    html/images/CAT.png
A  +    html/images/CAT_surf_atlas_DKT40.png
A  +    html/images/CAT_surf_atlas_Desikan-Killiany.png
A  +    html/images/CAT_surf_atlas_PALS-B12-Brodmann.png
A  +    html/images/CAT_surf_atlas_PALS-B12-Lobes.png
A  +    html/images/CAT_surf_atlas_aal.png
A  +    html/images/CAT_surf_atlas_hammers.png
A  +    html/images/CAT_surf_atlas_lpba40.png
A  +    html/images/CAT_surf_atlas_mori.png
A  +    html/images/CAT_surf_atlas_neuromorphometics.png
A  +    html/images/analyse_methods.png
A       html/images/background_biasreal.png
A       html/images/background_morphops.png
A       html/images/background_noise.png
A       html/images/cat_extract_addition_surface_parameter.png
A  +    html/images/cat_qa_expert.png
A  +    html/images/cat_qa_rating-distribution.png
A  +    html/images/cat_qa_rating-table.jpg
A       html/images/catreport_Collins.jpg
A  +    html/images/contact.jpg
A  +    html/images/cortical_measures.png
A  +    html/images/gyrification_index.png
A  +    html/images/home.jpg
A  +    html/images/human_brain.png
A  +    html/images/images.jpg
A  +    html/images/people.jpg
A       html/images/preprocessing.png
A  +    html/images/research.jpg
A  +    html/images/vbm.jpg
D       html/images.jpg
D       html/people.jpg
D       html/research.jpg
D       html/rqa01-intro-bwp-real.png
M       html/style.css
D       html/vbm.jpg
!       html/vbm_vol_correct_slice_scaling_768.png

Changed*:   Set cat_defaults extopts.BVCstr to 0, because of problems in
            untypical subjects, where artifacts were detected as BV and parts
            of the GM were removed.
Changed:    Added BVCstr parameter in expert GUI.
Changed:    Updated HTLM Help of VBM-Tools, SBM-Tools.
Changed:    Added HTML subdirectory for images.
Changed:    Renamed "CAT12" HTML breadcrumbs to "CAT".

------------------------------------------------------------------------
r864 | gaser | 2016-02-18 10:16:31 +0100 (Thu, 18 Feb 2016) | 34 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       html/cat.html
M       html/cat_FAQ.html
M       html/cat_ackknowledgement.html
M       html/cat_instruction_templates.html
M       html/cat_introduction.html
M       html/cat_methods.html
M       html/cat_methods_CAT.html
M       html/cat_methods_FN.html
M       html/cat_methods_LP.html
M       html/cat_methods_MS.html
M       html/cat_methods_QA.html
M       html/cat_methods_RBM.html
M       html/cat_methods_SBM.html
M       html/cat_methods_VBM.html
M       html/cat_methods_templates.html
 M      html/cat_qa_expert.png
 M      html/cat_qa_rating-distribution.png
 M      html/cat_qa_rating-table.jpg
M       html/cat_starting.html
M       html/cat_stuff.html
M       html/cat_tools.html
M       html/cat_tools_FF.html
M       html/cat_tools_ROI.html
M       html/cat_tools_SBM.html
M       html/cat_tools_VBM.html

Changed: Updated html-files:
 - Removed target="blank" that unnecessarily opens a matlab window
 - Use of matlab browser command throughout the pages

------------------------------------------------------------------------
r863 | gaser | 2016-02-17 23:11:48 +0100 (Wed, 17 Feb 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_stat_spmF2x.m
M       cat_stat_spmT2x.m

Fixed: Issues with correction for non-isotropy in cat_stat_spm[TF].m

------------------------------------------------------------------------
r862 | dahnke | 2016-02-12 17:51:08 +0100 (Fri, 12 Feb 2016) | 10 lines

Changed paths:
M       CHANGES.txt
 M      html/cat_methods_MS.html
A       html/cat_methods_templates.html
 M      html/cat_tools_FF.html
A       html/cat_tools_ROI.html
A       html/cat_tools_VBM.html

Changed:    Some further HTLM help pages.

------------------------------------------------------------------------
r861 | dahnke | 2016-02-12 17:49:37 +0100 (Fri, 12 Feb 2016) | 39 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
A       cat_io_addwarning.m
M       cat_main.m
A       cat_main_LAS.m
A       cat_main_gcut.m
A       cat_main_gintnorm.m
A       cat_main_gintnormi.m
M       cat_run_job.m
M       cat_surf_resamp.m
M       cat_surf_surf2roi.m
A       cat_vol_div.m
A       cat_vol_grad.m
M       html/cat.html
M       html/cat.txt
D       html/cat_instruction.html
D       html/cat_instruction_FF.html
D       html/cat_instruction_FN.html
D       html/cat_instruction_MS.html
D       html/cat_instruction_PP.html
D       html/cat_instruction_QA.html
D       html/cat_instruction_ST.html
!       html/cat_instruction_templates.html
M       html/cat_methods.html
A  +    html/cat_methods_FN.html
M       html/cat_methods_LP.html
A       html/cat_methods_MS.html
M       html/cat_starting.html
A  +    html/cat_tools.html
A       html/cat_tools_FF.html
A  +    html/cat_tools_SBM.html
M       internal/cat_vol_nlmus.m

Changed*:     Outsourced cat_main subfunctions and add some header comments.
Changed*:     Updated CAT help structure.
Changed:      Added comments in cat_surf_surf2roi.


------------------------------------------------------------------------
r860 | gaser | 2016-02-12 16:45:25 +0100 (Fri, 12 Feb 2016) | 13 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_long_main.m
M       cat_run.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Changed: Added again "native" field for GM/WM because it caused many
    problems in longitudinal batch.
(2) Updated: Longitudinal mode.


------------------------------------------------------------------------
r859 | dahnke | 2016-02-11 17:42:59 +0100 (Thu, 11 Feb 2016) | 44 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_io_FreeSurfer.m
M       cat_main.m
M       cat_run.m
M       cat_run_job.m
M       cat_stat_marks.m
M       cat_surf_surf2roi.m
M       html/cat.txt
A  +    html/cat_methods_CAT.html
M       html/cat_methods_QA.html
M       html/cat_methods_RBM.html
A       html/cat_qa_expert.png
A       html/cat_qa_rating-distribution.png
A       html/cat_qa_rating-table.jpg

Changed*:     Removed histogram scaling. Its working in principle, but it to
              strong depend on the data and requires further knowledge that
              turns it into another APP processing.
Changed*:     Commented gcut2 skull-stripping after second SPM preprocessing
              because it requires further adaptions and tests.
Changed*:     Catch errors only if extopts.debug>0 and for MATLAB>2007b and
              call cat_run_job directly.
Changed:      Update QA help text and added some figures.
Changed:      Removed CAT:cat_main:NCR error message because this is part of the
              QA and not required here anymore.
Changed:      Changed CAT:cat_main:UnknownContrast from warning to error
              because the resulting segmentation will differ to strongly from
              the standard CAT pipeline.
Changed:      Further preparation of cat_surf2roi (expert only) that runs now
              on a basic level.
Changed:      Updated QA rating in the CAT report. Display now the percentage
              rating points (rps) and the letter grad with .
Corrected*:   Added check of the initial affine registration with fall back to
              default registration to correct problems especially in skull-
              stripped images.
Corrected:    Changed CSF proportion (res.mg) from 10 to 30 percent for mean CSF
              peak estimation because of problems in images with high amount of
              blood vessels. Corrected initial Ym background value estimation.
Corrected:    CAT report Yo scaling failed in 5-10% of test cases, because the
              SPM peaks of Ym differ to much.

------------------------------------------------------------------------
r858 | gaser | 2016-02-11 16:00:12 +0100 (Thu, 11 Feb 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       html/cat_instruction_FN.html
M       html/cat_instruction_PP.html
M       html/cat_instruction_templates.html

Fixed: Some broken links and calls in html-pages.


------------------------------------------------------------------------
r857 | gaser | 2016-02-11 12:37:13 +0100 (Thu, 11 Feb 2016) | 22 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_defaults.m
M       cat_main.m
M       cat_surf_createCS.m
M       cat_surf_parameters.m
M       html/cat_instruction_FN.html
M       html/cat_instruction_PP.html
M       html/cat_starting.html
M       tbx_cfg_cat.m

(1) Changed: Many updates in html-pages.
(2) Fixed: Wrong name fur sulcus data in cat_surf_parameters.m.
(3) Fixed: Wrong use of "~" in cat_surf_createCS.m.
(4) Changed: Default setting for ignoring errors set to "0".
(5) Fixed: Missing rounding for uint8 in cat_main.m.
(6) Changed: Updated CAT12-Manual.

------------------------------------------------------------------------
r856 | gaser | 2016-02-09 23:52:52 +0100 (Tue, 09 Feb 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_vol_slice_overlay.m

Fixed: Issue with && operator in cat_vol_slice_overlay.m

------------------------------------------------------------------------
r855 | dahnke | 2016-02-08 16:54:14 +0100 (Mon, 08 Feb 2016) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat12.fig
M       cat_main.m
M       cat_run_job.m
M       cat_surf_surf2roi.m
M       compile.m

Added:      Added functions test in for cat_vol_simgrow.c and cat_vol_downcut.c
            in compile.m function.
Update:     Modified histogram limitation in APP==0 (default) processing.
            Try to correct errors in background estimation for masked data
            ("Only nonempty 3D volumes!" error in cat_main line ~468).
Added:      Added Help call in GUI>Internet/Help that (re)open CAT Help in
            SPM Graphics window.


------------------------------------------------------------------------
r854 | gaser | 2016-02-08 09:04:43 +0100 (Mon, 08 Feb 2016) | 51 lines

Changed paths:
M       CAT12-Manual.doc
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_amap.mexmaci64
M       cat_amap.mexw64
M       cat_ornlm.mexmaci64
M       cat_ornlm.mexw64
M       cat_sanlm.mexa64
M       cat_sanlm.mexmaci64
M       cat_sanlm.mexw64
M       cat_vbdist.mexa64
M       cat_vbdist.mexmaci64
M       cat_vbdist.mexw64
M       cat_vol_downcut.mexmaci64
M       cat_vol_downcut.mexw64
M       cat_vol_eidist.mexa64
M       cat_vol_eidist.mexw64
M       cat_vol_genus0.mexmaci64
M       cat_vol_genus0.mexw64
M       cat_vol_gradient3.c
M       cat_vol_gradient3.mexa64
M       cat_vol_gradient3.mexmaci64
M       cat_vol_gradient3.mexw64
M       cat_vol_interp3f.mexmaci64
M       cat_vol_interp3f.mexw64
M       cat_vol_laplace3.mexmaci64
M       cat_vol_laplace3.mexw64
M       cat_vol_laplace3R.mexmaci64
M       cat_vol_laplace3R.mexw64
M       cat_vol_localstat.mexmaci64
M       cat_vol_localstat.mexw64
M       cat_vol_median3.mexmaci64
M       cat_vol_median3.mexw64
M       cat_vol_median3c.mexmaci64
M       cat_vol_median3c.mexw64
M       cat_vol_pbtp.mexmaci64
M       cat_vol_pbtp.mexw64
M       cat_vol_simgrow.mexmaci64
M       cat_vol_simgrow.mexw64
M       compile.m
M       html/cat.html
M       sanlm_float.c

(1) Fixed: Some typos.
(2) Fixed: Wrong brackest in cat_vol_gradient3.c.
(3) Changed: Makefile
(4) Changed: Commented out output of # of processors in sanlm_float.c
(5) Fixed: compile.m that was using Robert-specific code

------------------------------------------------------------------------
r853 | gaser | 2016-02-04 10:27:56 +0100 (Thu, 04 Feb 2016) | 16 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       cat_tst_qa.m
M       cat_vol_atlas.m
M       cat_vol_morph.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Fixed: Some typos.
(2) Changed: If lab in cat_vol_morph.m fails then return empty parameter to
    inidicate that something failed.
(3) Changed: Stop if lab in cat_vol_morph.m fails and give error message
    that normalization likeli failed.

------------------------------------------------------------------------
r852 | gaser | 2016-02-02 17:33:30 +0100 (Tue, 02 Feb 2016) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       cat_run.m
M       cat_run_job.m
M       html/cat.html
M       tbx_cfg_cat.m

Changed: Some minor bug fixes and edits.

------------------------------------------------------------------------
r851 | dahnke | 2016-02-02 14:57:08 +0100 (Tue, 02 Feb 2016) | 26 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_main.m
M       cat_run_job.m
M       cat_stat_marks.m
A       cat_surf_surf2roi.m
M       cat_vol_resize.m

Corrected:      Fixed error "spm_affreg.line474.insufficient image overlap"
                caused by bad scaling of MT data in cat_run_job.
Corrected:      Fixed error "cat_main.line1812.cleared variable."
Corrected:      Structure order output error.
Updated:        Modified histogram-based intensity limitation.
Updated:        Removed QA rating defaults from CAT report.
                Added APP, WMHC, WMHCstr parameter to CAT expert report.
                Moved expert warnings to QA side.
Updated:        Corrected bias worst case value.
Changed:        Lower ORNLM noise setting. Set cat_defaults extopts.sanlm=1
                (only sanlm filtering, but multiple times).
Added:          Prepared cat_surf_surf2roi function and GUI.




------------------------------------------------------------------------
r850 | gaser | 2016-02-01 16:29:38 +0100 (Mon, 01 Feb 2016) | 19 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       Contents.m
M       cat_batch_vbm.m
M       cat_main.m
M       cat_run.m
M       cat_run_job.m
M       html/cat.html

(1) Changed: Updated batch mode to consider expert mode.
(2) Fixed: Replaced std with cat_stat_nanstd and fixed wrong data-field
    in cat_run_job.m.
(3) Fixed: Updated cat_run.m to consider fields that are only available
    in expert mode.
(4) Changed: Cleared many unnecessary variables with large memory demand.
(5): Changed: Updated CAT12-Manual.

------------------------------------------------------------------------
r849 | dahnke | 2016-01-29 18:09:48 +0100 (Fri, 29 Jan 2016) | 25 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_main.m
M       cat_run_job.m
M       cat_run_newcatch.m
M       cat_run_oldcatch.m
M       cat_stat_marks.m
M       cat_surf_vol2surf.m
M       cat_tst_qa.m
M       cat_vol_resize.m

Changed:    Added APP0 (SPM default) intensity limits (2%-98%) to avoid problems
            for untypical (high) intensities in synthetical T1 images.
Corrected:  Corrected CSF brain extraction threshold of SPM segments background
            as CSF that was finally the larges component and cause removing of
            the brain rather noise background segments.
Corrected:  Optimized error directory output name in cat_run_[old|new]catch.
Corrected:  First QA update.
Corrected:  Problem in LAS for negative CSF intensities.
Removed:    Removed old uncommented code.
Updated:    Native-space Vol2surf GUI and function.



------------------------------------------------------------------------
r848 | gaser | 2016-01-29 15:50:48 +0100 (Fri, 29 Jan 2016) | 37 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_vbm.m
M       cat_run.m
M       html/cat.html
 M      templates_surfaces/lh.PALS_B12_Brodmann.freesurfer.annot
 M      templates_surfaces/lh.PALS_B12_Lobes.freesurfer.annot
 M      templates_surfaces/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M      templates_surfaces/lh.PALS_B12_Visuotopic.freesurfer.annot
 M      templates_surfaces/lh.aal.Template_T1_IXI555_MNI152
 M      templates_surfaces/lh.aparc.freesurfer.annot
 M      templates_surfaces/lh.aparcDKT40.freesurfer.annot
 M      templates_surfaces/lh.aparcDKT40JT.freesurfer.annot
 M      templates_surfaces/lh.aparc_a2005s.freesurfer.annot
 M      templates_surfaces/lh.aparc_a2009s.freesurfer.annot
 M      templates_surfaces/lh.hammers.Template_T1_IXI555_MNI152
 M      templates_surfaces/lh.lpba40.Template_T1_IXI555_MNI152
 M      templates_surfaces/lh.mori.Template_T1_IXI555_MNI152
 M      templates_surfaces/lh.neuromorphometrics.Template_T1_IXI555_MNI152
 M      templates_surfaces/rh.PALS_B12_Brodmann.freesurfer.annot
 M      templates_surfaces/rh.PALS_B12_Lobes.freesurfer.annot
 M      templates_surfaces/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
 M      templates_surfaces/rh.PALS_B12_Visuotopic.freesurfer.annot
 M      templates_surfaces/rh.aal.Template_T1_IXI555_MNI152
 M      templates_surfaces/rh.aparc.freesurfer.annot
 M      templates_surfaces/rh.aparcDKT40.freesurfer.annot
 M      templates_surfaces/rh.aparcDKT40JT.freesurfer.annot
 M      templates_surfaces/rh.aparc_a2005s.freesurfer.annot
 M      templates_surfaces/rh.aparc_a2009s.freesurfer.annot
 M      templates_surfaces/rh.hammers.Template_T1_IXI555_MNI152
 M      templates_surfaces/rh.lpba40.Template_T1_IXI555_MNI152
 M      templates_surfaces/rh.mori.Template_T1_IXI555_MNI152
 M      templates_surfaces/rh.neuromorphometrics.Template_T1_IXI555_MNI152

Changed: Updated batch mode.

------------------------------------------------------------------------
r847 | gaser | 2016-01-28 21:42:23 +0100 (Thu, 28 Jan 2016) | 10 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat_stat_check_cov.m
M       html/cat_methods_VBM.html

(1) Changed: Updated manual.
(2) Changed: Removed violin plot from cat_stat_check_cov.m

------------------------------------------------------------------------
r846 | gaser | 2016-01-28 14:23:42 +0100 (Thu, 28 Jan 2016) | 20 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_defaults.m
M       cat_main.m
M       cat_update.m
M       cat_vol_display_label.m
A  +    html/CAT_surf_atlas_Desikan-Killiany.png
D       html/CAT_surf_atlas_Deskan-Killiany.png
M       html/cat.html
M       html/cat_instruction_PP.html
M       html/cat_methods_RBM.html
M       tbx_cfg_cat.m

(1) Changed: Moved some options from tbx_cfg_cat.m to expert mode.
(2) Fixed: Deskan->Desikan in html
(3) Fixed: Many, many typos.
(4) Fixed: Reoplaced nanmax/nanmin in cat_vol_display_label.m


------------------------------------------------------------------------
r845 | gaser | 2016-01-27 13:04:22 +0100 (Wed, 27 Jan 2016) | 10 lines

Changed paths:
M       CAT12-Manual.doc
M       CAT12-Manual.pdf
M       CHANGES.txt
M       cat12.m
MM      templates_1.50mm/cobra.txt

(1) Fixed: Issue with fixed filename in metadata field in cat12.m.
(2) Changed: Updated manual which is not yet finished.

------------------------------------------------------------------------
r844 | dahnke | 2016-01-26 15:13:34 +0100 (Tue, 26 Jan 2016) | 54 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_display.m
M       cat_surf_info.m
M       cat_surf_rename.m
M       cat_surf_render.m
A       html/CAT_surf_atlas_DKT40.png
A       html/CAT_surf_atlas_Deskan-Killiany.png
A       html/CAT_surf_atlas_PALS-B12-Brodmann.png
A       html/CAT_surf_atlas_PALS-B12-Lobes.png
A       html/CAT_surf_atlas_aal.png
A       html/CAT_surf_atlas_hammers.png
A       html/CAT_surf_atlas_lpba40.png
A       html/CAT_surf_atlas_mori.png
A       html/CAT_surf_atlas_neuromorphometics.png
M       html/cat_methods_RBM.html
A       templates_surfaces/lh.PALS_B12_Brodmann.freesurfer.annot
A       templates_surfaces/lh.PALS_B12_Lobes.freesurfer.annot
A       templates_surfaces/lh.PALS_B12_OrbitoFrontal.freesurfer.annot
A       templates_surfaces/lh.PALS_B12_Visuotopic.freesurfer.annot
A       templates_surfaces/lh.aal.Template_T1_IXI555_MNI152
A       templates_surfaces/lh.aparc.freesurfer.annot
A       templates_surfaces/lh.aparcDKT40.freesurfer.annot
A       templates_surfaces/lh.aparcDKT40JT.freesurfer.annot
A       templates_surfaces/lh.aparc_a2005s.freesurfer.annot
A       templates_surfaces/lh.aparc_a2009s.freesurfer.annot
A       templates_surfaces/lh.hammers.Template_T1_IXI555_MNI152
A       templates_surfaces/lh.lpba40.Template_T1_IXI555_MNI152
A       templates_surfaces/lh.mori.Template_T1_IXI555_MNI152
A       templates_surfaces/lh.neuromorphometrics.Template_T1_IXI555_MNI152
A       templates_surfaces/rh.PALS_B12_Brodmann.freesurfer.annot
A       templates_surfaces/rh.PALS_B12_Lobes.freesurfer.annot
A       templates_surfaces/rh.PALS_B12_OrbitoFrontal.freesurfer.annot
A       templates_surfaces/rh.PALS_B12_Visuotopic.freesurfer.annot
A       templates_surfaces/rh.aal.Template_T1_IXI555_MNI152
A       templates_surfaces/rh.aparc.freesurfer.annot
A       templates_surfaces/rh.aparcDKT40.freesurfer.annot
A       templates_surfaces/rh.aparcDKT40JT.freesurfer.annot
A       templates_surfaces/rh.aparc_a2005s.freesurfer.annot
A       templates_surfaces/rh.aparc_a2009s.freesurfer.annot
A       templates_surfaces/rh.hammers.Template_T1_IXI555_MNI152
A       templates_surfaces/rh.lpba40.Template_T1_IXI555_MNI152
A       templates_surfaces/rh.mori.Template_T1_IXI555_MNI152
A       templates_surfaces/rh.neuromorphometrics.Template_T1_IXI555_MNI152

Added:      Added FreeSurfer surface atlas maps (annotation maps).
Added:      Added CAT12 volume-based surface atlas maps (gifti) as FS data files.
Updated:    Added temporary colormaps for visualization of volume atlas maps in
            cat_surf_display.
Changed:    Set PNG as standard "save as" in cat_surf_display.
Changed:    Added further informations, images and links in ROI XML help.



------------------------------------------------------------------------
r843 | gaser | 2016-01-25 22:17:34 +0100 (Mon, 25 Jan 2016) | 9 lines

Changed paths:
M       CHANGES.txt
MM      cat_parallelize.m

(1) Removed: cat_stat_spm.m because we now always use spm_spm.m and modify
    SPM.mat according to underlying fsaverage surface from freesurfer.
(2) Removed: Field extopts.gui because we will always use CAT12 in GUI mode.
(3) Changed: All files that are affected by the above mentioned changes.

------------------------------------------------------------------------
r842 | gaser | 2016-01-25 22:17:15 +0100 (Mon, 25 Jan 2016) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_batch_vbm.m
M       cat_defaults.m
D       cat_stat_spm.m
M       spm_cat12.m

(1) Removed: cat_stat_spm.m because we now always use spm_spm.m and modify
    SPM.mat according to underlying fsaverage surface from freesurfer.
(2) Removed: Field extopts.gui because we will always use CAT12 in GUI mode.
(3) Changed: All files that are affected by the above mentioned changes.

------------------------------------------------------------------------
r841 | gaser | 2016-01-25 14:53:04 +0100 (Mon, 25 Jan 2016) | 24 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_stools.m
M       cat_main.m
M       cat_stat_spm.m
M       cat_surf_parameters.m
M       cat_surf_render.m
M       cat_surf_resamp.m
M       cat_surf_resample.m
M       cat_surf_smooth.m
M       html/cat.html
M       html/cat_starting.html
M       templates_1.50mm/cobra.csv
M       templates_1.50mm/cobra.nii
A       templates_1.50mm/cobra.txt
M       templates_1.50mm/labels_dartel_cobra.xml

(1) Fixed: Added metadata field with filename in CAT-gifti functions.
(2) Fixed: Some typos in cat_main.m
(3) Changed: Merged some hippocampus subfields (CA1/CA2/CA3/Stratum/Subiculum) in cobra.atlas.
(4) Added: Option for changing underlying geometry in cat_surf_render.m


------------------------------------------------------------------------
r840 | dahnke | 2016-01-22 16:06:59 +0100 (Fri, 22 Jan 2016) | 54 lines

Changed paths:
M       CHANGES.txt
M       cat_check_system_output.m
M       cat_conf_stools.m
M       cat_defaults.m
M       cat_io_FreeSurfer.m
M       cat_io_writenii.m
M       cat_main.m
A       cat_parallelize.m
M       cat_plot_boxplot.m
M       cat_run_job.m
M       cat_run_newcatch.m
M       cat_run_oldcatch.m
M       cat_surf_calc.m
M       cat_surf_display.m
M       cat_surf_info.m
M       cat_surf_parameters.m
M       cat_surf_render.m
M       cat_surf_resamp.m
M       cat_surf_resample.m
M       cat_surf_smooth.m
M       cat_surf_vol2surf.m
M       internal/cat_vol_atlas.m
M       tbx_cfg_cat.m

Added:      Created cat_parallelize as common function to create separate
            processes on one computer (default GUI).
Added:      Parallelized cat_surf_parameter and add further parameter.
Updated:    cat_surf_resamp/resample/smooth/parameters and cat_main
            for new cat_parallelize function.

Added:      Create a subfolder 'err' for failed preprocessing with copies of
            the cat-xml and cat_report to identify problematic datasets in
            cat_run_newcatch/cat_run_oldcatch.
Added:      Added display option rather create error in cat_check_system_ouput.
Added:      Folder creation in cat_io_writenii, if a result directory not exist.

Added:      FreeSurfer annotation input in cat_io_FreeSurfer.
Added:      Display of Freesurfer annotation display in cat_surf_display/
            cat_surf_render.
Added:      Output of atlas maps in cat_main.
Added:      Optional use of fsaverage mesh in cat_surf_calc.
Added:      Added GIFTI to FreeSurfer and FreeSurfer to GIFTI convertation in
            cat_io_FreeSurfer.

Updated:    Improved scaling function in cat_plot_boxplot.








------------------------------------------------------------------------
r839 | gaser | 2016-01-22 11:59:17 +0100 (Fri, 22 Jan 2016) | 13 lines

Changed paths:
M       CAT12-Manual.doc
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_plot_circular.m
M       cat_surf_display.m
M       cat_surf_info.m
M       cat_surf_parameters.m

(1) Changed: Added font size option to cat_plot_circular.m
(2) Changed: Changed use of log-transformation to sqrt-transformation for
    estimating sulcus depth. Changed all filenames from logsulc to sqrtsulc.

------------------------------------------------------------------------
r838 | gaser | 2016-01-22 00:32:47 +0100 (Fri, 22 Jan 2016) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_io_csv.m
M       cat_io_writenii.m
M       cat_main.m
M       cat_vol_findfiles.m

(1) Fixed: Some typos in help textes.
(2) Removed: Unnecessary fields in cat_conf_tools.m that are already
    included in cat_conf_stools.m.

------------------------------------------------------------------------
r837 | gaser | 2016-01-20 21:31:48 +0100 (Wed, 20 Jan 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
MM      cat_stat_cva_ui.m
M       html/cat_instruction_FN.html

Changed: Help text in cat_conf_tools.m and html/cat_instruction_FN.html.

------------------------------------------------------------------------
r836 | gaser | 2016-01-20 20:48:14 +0100 (Wed, 20 Jan 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_plot_boxplot.m
M       cat_stat_check_cov.m
M       cat_stat_cva_ui.m

Fixed: Violine plot in cat_plot_boxplot will be only used if Statistics
Toolbox is found.

------------------------------------------------------------------------
r835 | gaser | 2016-01-18 22:52:48 +0100 (Mon, 18 Jan 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
MM      cat_plot_circular.m
A       cat_stat_cva_ui.m
M       html/cat.html

New: Function for CVA.

------------------------------------------------------------------------
r834 | gaser | 2016-01-18 14:26:38 +0100 (Mon, 18 Jan 2016) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_plot_circular.m
M       cat_stat_TIV.m
M       cat_surf_render.m

(1) Fixed: Issue with missing "ned" in cat_surf_render.m.
(2) Fixed: Wrong order of tissues in cat_stat_TIV.m (thanks to Nikolaos
    Koutsouleris for pointing to that issues)
(3) Changed: Added some more functionality to cat_plot_circular.m

------------------------------------------------------------------------
r833 | gaser | 2016-01-17 23:23:32 +0100 (Sun, 17 Jan 2016) | 14 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
M       cat_io_checkinopt.m
M       cat_plot_circular.m
M       cat_version.m
M       cat_vol_defs.m

(1) Fixed: Correct handling of filetypes and 4D-data in cat_vol_defs.m
(2) Fixed: If Contents.txt does not exist serach for Contens.m in cat_version.m
(3) Fixed: Correct handling of outputs in cat_conf_tools.m for applying
    deformations.
(4) Added some more features in cat_plot_circular.

------------------------------------------------------------------------
r832 | gaser | 2016-01-14 17:08:42 +0100 (Thu, 14 Jan 2016) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_plot_boxplot.m
A       cat_plot_circular.m
D       circularGraph.m
D       node.m

(1) Added: New circular plot cat_plot_circular.m.
(2) Deleted: circularGraph.m and node.m

------------------------------------------------------------------------
r831 | gaser | 2016-01-14 15:00:03 +0100 (Thu, 14 Jan 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_plot_boxplot.m
M       html/cat.html

Changed: added violin-plot for cat_plot_boxplot.m and added and changed
some defaults.

------------------------------------------------------------------------
r830 | gaser | 2016-01-14 11:44:36 +0100 (Thu, 14 Jan 2016) | 13 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_surf_render.m
M       cat_surf_vol2surf.m
M       tbx_cfg_cat.m
 M      templates_1.50mm/cobra.csv
 M      templates_1.50mm/cobra.nii
 M      templates_1.50mm/labels_dartel_cobra.xml

(1) Changed: defaults for atlases.
(2) Fixed: number of regions for lpba40 is 56.

------------------------------------------------------------------------
r829 | dahnke | 2016-01-12 12:39:00 +0100 (Tue, 12 Jan 2016) | 26 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_main.m
M       cat_surf_createCS.m
M       cat_surf_display.m
M       cat_surf_info.m
M       cat_surf_resamp.m
M       cat_surf_resample.m
M       cat_surf_smooth.m
M       cat_vol_pbt.m
M       tbx_cfg_cat.m

Removed:    Removed subject space ROI analysis, because (i) it was to specific
            for some atlas maps, (ii) the missing systematic evaluation, (iii)
            only small improvement that did not correct major hinds of some
            atlas maps.
Removed:    Deleted other old code segments and functions.
Updated:    ROI analysis text.
Changed:    Changed CSF/WM depth measures (span/width/thickness of CSF/WM),
            because of problems showed up after the last major corrections.
Changed:    Changed handling of background in PBT to avoid surface mapping
            problems.
Fixed:      Corrected smaller errors in cat_surf_resamp/resample/smooth.


------------------------------------------------------------------------
r828 | gaser | 2016-01-08 10:20:30 +0100 (Fri, 08 Jan 2016) | 17 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_long_multi_run.m
M       cat_main.m
M       cat_run.m
M       cat_run_job.m
M       cat_version.m
M       html/cat.html
A       templates_1.50mm/cobra.csv
A       templates_1.50mm/cobra.nii
A       templates_1.50mm/labels_dartel_cobra.xml

(1) Changed: cat_version.m should search for Contents.txt to conisder
    compiled code.
(2) Fixed: Longitudinal mode was not yet prepared for subfolders.

------------------------------------------------------------------------
r827 | dahnke | 2016-01-07 16:58:40 +0100 (Thu, 07 Jan 2016) | 20 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_opts.m
M       cat_conf_stools.m
M       cat_run.m
M       cat_surf_createCS.m
M       cat_surf_display.m
M       cat_surf_info.m
M       cat_surf_resamp.m
M       cat_surf_resample.m
M       cat_surf_smooth.m
MM      cat_vol_display_label.m

Fixed:    Corrected WM width correction.
Changed:  Added progress bar, output variable with result files, linked command
          line output, verb option, and parallel processing to
          cat_surf_resample, cat_surf_smooth, and cat_surf_resamp.
Changed:  Set logdate to YYYYmmdd_HHMMSS to have time ordered log-files.
Changed:  Automatic delay for opening of parallel processing log files.

------------------------------------------------------------------------
r826 | dahnke | 2016-01-05 10:56:41 +0100 (Tue, 05 Jan 2016) | 41 lines

Changed paths:
 M      .
M       CHANGES.txt
M       cat_defaults.m
M       cat_io_FreeSurfer.m
M       cat_main.m
M       cat_run_job.m
M       cat_surf_createCS.m
M       cat_vbdist.c
M       cat_vbdist.mexmaci64
M       cat_version.m
M       cat_vol_atlas.m
A       cat_vol_display_label.m
M       compile.m
M       html/cat_methods_RBM.html
M       templates_1.50mm/labels_dartel_neuromorphometrics.xml
M       templates_1.50mm/neuromorphometrics.csv
M       templates_1.50mm/neuromorphometrics.nii

Fixed:    Corrected GCUT (GUI) parameter input.
Fixed:    Labeling of Neuromorphometics atlas map.
Fixed:    >255 warning only once in cat_vbdist.
Fixed:    Corrected subdir writing error.
Changed:  Added APP ... gcut parameter
Changed:  Cleanup resolution threshold to 2.2 mm.
Changed:  Preliminary update of skull-stripping functions:
          * Added the gcut-parameter in APP.
            APP should create a wide mask that have to include the brain in
            any case and in cost of including head tissue!
          * Replaced initial skull-stripping after SPM segmentation by GCUT2.
          * Updated gcut subparamters with head and relative volume information.
            E.g. smaller heads (primates) required a smaller closing whereas
            older brains with big ventricle requires a larger closing.
          * Extensive tests are still required!
Changed:  Added help in cat_io_FreeSurfer
New:      cat_vol_display_label function based on cg_addtruecolorimage, for one
          background and multiple overlay images. Added calls in CAT help
          (CAT12 > Methods > Atlas creation and ROI based analysis).



------------------------------------------------------------------------
r825 | gaser | 2015-12-22 16:50:35 +0100 (Tue, 22 Dec 2015) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_render.m
M       html/cat.html

Added: Options to clip cdata abd to allow slider context menu in
cat_surf_render.m

------------------------------------------------------------------------
r824 | gaser | 2015-12-22 16:47:40 +0100 (Tue, 22 Dec 2015) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
 M      circularGraph.m
M       html/cat.html
 M      node.m

Added: Options to clip cdata abd to allow slider context menu in
cat_surf_render.m

------------------------------------------------------------------------
r823 | gaser | 2015-12-22 16:37:06 +0100 (Tue, 22 Dec 2015) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_surf_render.m
M       html/cat.html

Added: Options to clip cdata abd to allow slider context menu in
cat_surf_render.m

------------------------------------------------------------------------
r822 | gaser | 2015-12-22 12:20:23 +0100 (Tue, 22 Dec 2015) | 9 lines

Changed paths:
M       CHANGES.txt
A       circularGraph.m
A       node.m

(1) Added: Some preliminary functions fpr circular draws.
(2) Added: CAT_Vol2Surf to save filled volume inside a surface.
(3) Changed: Recompiled code.

------------------------------------------------------------------------
r821 | gaser | 2015-12-22 09:03:22 +0100 (Tue, 22 Dec 2015) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m

Fixed: Removed bug in cat_surf_createCS.m where the pp* files were not
correctly saved in the mri subfolder.

------------------------------------------------------------------------
r820 | gaser | 2015-12-21 15:16:48 +0100 (Mon, 21 Dec 2015) | 22 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_io_writenii.m
M       cat_main.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_newcatch.m
M       cat_run_oldcatch.m
M       cat_stat_calc_stc.m
M       cat_surf_createCS.m
M       cat_tst_qa.m
 M      templates_surfaces/lh.mask.txt
 M      templates_surfaces/lh.rois.a2009s.txt
 M      templates_surfaces/rh.mask.txt
 M      templates_surfaces/rh.rois.a2009s.txt
 M      templates_surfaces/rois.a2009s.txt
 M      templates_surfaces/templates_surfaces.man

Changed: Added option to save results in subfolders such as mri, surf, label
and report. All resp. files were changed to allow subfolders.

------------------------------------------------------------------------
r819 | gaser | 2015-12-18 16:26:17 +0100 (Fri, 18 Dec 2015) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_conf_extopts.m
M       html/cat.html
M       tbx_cfg_cat.m
 M      templates_1.50mm/labels_dartel_aal.xml
 M      templates_1.50mm/labels_dartel_hammers.xml
 M      templates_1.50mm/labels_dartel_ibsr.xml
 M      templates_1.50mm/labels_dartel_lpba40.xml
 M      templates_1.50mm/labels_dartel_mori.xml
 M      templates_1.50mm/labels_dartel_neuromorphometrics.xml

Changed: Some minor typo correction.

------------------------------------------------------------------------
r818 | gaser | 2015-12-18 14:39:20 +0100 (Fri, 18 Dec 2015) | 23 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_conf_stoolsexp.m
M       cat_surf_info.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
MM      cat_version.m
A       templates_surfaces/lh.mask.txt
A       templates_surfaces/lh.rois.a2009s.txt
A       templates_surfaces/rh.mask.txt
A       templates_surfaces/rh.rois.a2009s.txt
A       templates_surfaces/rois.a2009s.txt
A       templates_surfaces/templates_surfaces.man

(1) Changed: Added support for NaN values for smoothing after resampling.
    This utilizez masked smoothing and skipping those areas from
    statistical analysis.
(2) Changed: Removed call of redundant cat_surf_resample.m.
(3) Changed: Added spm-input option if no hemisphere information can be found
    in cat_surf_display.m (e.g. for results of statistical analysis).


------------------------------------------------------------------------
r817 | dahnke | 2015-12-17 15:27:24 +0100 (Thu, 17 Dec 2015) | 40 lines

Changed paths:
M       CHANGES.txt
M       cat_install_atlases.m
M       cat_main.m
M       cat_surf_createCS.m
M       cat_vol_atlas.m
M       cat_vol_resize.m
M       templates_1.50mm/aal.csv
M       templates_1.50mm/aal.txt
M       templates_1.50mm/hammers.csv
M       templates_1.50mm/hammers.nii
M       templates_1.50mm/hammers.txt
M       templates_1.50mm/ibsr.csv
M       templates_1.50mm/ibsr.nii
M       templates_1.50mm/ibsr.txt
D       templates_1.50mm/label_dartel_aal.xml
D       templates_1.50mm/label_dartel_hammers.xml
D       templates_1.50mm/label_dartel_ibsr.xml
D       templates_1.50mm/label_dartel_lpba40.xml
D       templates_1.50mm/label_dartel_mori.xml
D       templates_1.50mm/label_dartel_neuromorphometrics.xml
A       templates_1.50mm/labels_dartel_aal.xml
A       templates_1.50mm/labels_dartel_hammers.xml
A       templates_1.50mm/labels_dartel_ibsr.xml
A       templates_1.50mm/labels_dartel_lpba40.xml
A       templates_1.50mm/labels_dartel_mori.xml
A       templates_1.50mm/labels_dartel_neuromorphometrics.xml
M       templates_1.50mm/mori.csv
M       templates_1.50mm/mori.nii
M       templates_1.50mm/mori.txt
M       templates_1.50mm/neuromorphometrics.csv
M       templates_1.50mm/neuromorphometrics.nii
M       templates_1.50mm/neuromorphometrics.txt

Fixed:    Corrections in WM/CSF width estimation.
Fixed:    Corrected interpolation error in case of complete reduction of voxel
          resolution.
Fixed:    Corrected XML labeling in cat_vol_atlas and update atlas maps.
New:      Added ROI XYZ Coordinates (center of mass) in XML files.

------------------------------------------------------------------------
r816 | gaser | 2015-12-17 15:01:54 +0100 (Thu, 17 Dec 2015) | 6 lines

Changed paths:
M       CHANGES.txt
M       cat_tst_qa.m

Fixed: Correct version for SPM and CAT in cat_tst_qa.m.

------------------------------------------------------------------------
r815 | gaser | 2015-12-17 12:54:26 +0100 (Thu, 17 Dec 2015) | 24 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
MM      cat_install_atlases.m
M       cat_run_job.m
M       cat_surf_createCS.m
M       cat_tst_qa.m
M       cat_update.m
A       cat_version.m
M       html/cat.html
MM      internal/cat_surf_reduceAvgSurf.m
 M      internal/cat_vol_cMRegularizarNLM3D.c
 M      internal/cat_vol_cMRegularizarNLM3D.mexmaci64
 M      internal/cat_vol_cMRegularizarNLM3Dw.c
MM      internal/cat_vol_nlmus.m

(1) Added: cat_version.m that is reading the Content.txt that can be also read
    if SPM is in deployed mode (using the compiled version that prevents to
    read *.m files.
(2) Changed: replaced checks for CAT version using "ver" and use cat_version
    throughout.


------------------------------------------------------------------------
r814 | gaser | 2015-12-17 00:43:56 +0100 (Thu, 17 Dec 2015) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m

(1) Fixed: Removed testing functions in cat_surf_createCS.m
(2) Changed: Topology correction was not improved by using an initial threshold
    close to WM surface. Thus, we again use an inital threshold of 0.5 for
    the central surface and so some surface deformation.

------------------------------------------------------------------------
r813 | gaser | 2015-12-15 16:37:18 +0100 (Tue, 15 Dec 2015) | 14 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       cat_surf_createCS.m
M       cat_vol_eidist.c
M       cat_vol_eidist.mexmaci64
M       cat_vol_median3.c
M       html/cat.html

(1) Changed: Better use of PP map and optimized parameters
    for surface deformations.
(2) Changed: Cleaned some c-code (without affecting outputs).

------------------------------------------------------------------------
r812 | dahnke | 2015-12-14 10:56:42 +0100 (Mon, 14 Dec 2015) | 36 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_surf_createCS.m
M       cat_surf_display.m
M       cat_vol_atlas.m
M       cat_vol_pbt.m
M       cat_vol_sanlm.m
M       compile.m
 M      internal
A       internal/cat_surf_reduceAvgSurf.m
MM      internal/cat_vol_atlas.m
A       internal/cat_vol_cMRegularizarNLM3D.c
A       internal/cat_vol_cMRegularizarNLM3D.mexmaci64
A       internal/cat_vol_cMRegularizarNLM3Dw.c
A       internal/cat_vol_nlmus.m
 M      templates_surfaces

Fixed:    Small, but severe error in the thickness and surface position
          estimation of PBT2x.
Fixed:    Corrected errors in internal cat_vol_atlas.
Fixed:    Corrected thickness projection problem in low resolution data.
Fixed:    Corrected copy&paste-error of global thickness report.
Changed:  Added some code, if only one surface is available.
New:      Added Non-local-means upsampling (NLMUS) function cat_vol_nlmus.
          NLMUS is relatively slow (~10 minutes for 1x1x3 NIH image, ~40 minutes
          for 0.6x0.6x1.8 reduced Winterburn image), but I think it do a great
          job especially for anisotropic data. It does not work in label images
          such as the p0*.nii or atlas maps.
New:      Added internal c-function for NLMUS for mac/linux (working) and
          windows (not yet tested). Added code in compile function.
New:      Added internal function to reduce template surfaces for faster tests.
          Although the reduction works correct, moste surface processing
          functions were not faster.


------------------------------------------------------------------------
r811 | gaser | 2015-12-12 01:05:47 +0100 (Sat, 12 Dec 2015) | 10 lines

Changed paths:
M       CHANGES.txt
A       cat_install_atlases.m
M       cat_surf_createCS.m

(1) Changed: Surface creation now allows to start with WM surface and to
    estimate a preliminary central surface that is finally refined using
    surface deformation.
(2) Added: function to install atlases in SPM.

------------------------------------------------------------------------
r810 | gaser | 2015-12-11 16:57:14 +0100 (Fri, 11 Dec 2015) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_long.m
M       cat_batch_vbm.m
M       cat_surf_createCS.m
M       html/cat.html

(1) Fixed: CAT_NiftiIO now correctly reads nifti-files (affects mapping using
    CAT_3dVol2Surf and CAT_Deform).
(2) Fixed: Update of longitudinal batch to consider new matlab versions.

------------------------------------------------------------------------
r809 | dahnke | 2015-12-03 15:51:39 +0100 (Thu, 03 Dec 2015) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_run.m
M       cat_surf_createCS.m
M       cat_surf_vol2surf.m
M       cat_tst_qa.m
M       templates_animals/cat_defaults_monkey_oldworld.m

Changed:  Update CAT report by moving vx_vol to the parameter part and adding
          the internal resolution and the PBT resolution (in case of surface
          processing). Added the internal resolution also to CAT XML file.
Changed:  Set -nodesktop for system call in cat_run with nproc>0 to allow
          printing of figure such as the CAT report.
Fixed:    Workaround in cat_surf_vol2surf with MATLAB value extraction in case
          of simple readout at CS position.
Fixed:    Command Line output in cat_surf_createCS.


------------------------------------------------------------------------
r808 | dahnke | 2015-12-03 10:19:36 +0100 (Thu, 03 Dec 2015) | 31 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_run.m
M       cat_surf_createCS.m
M       cat_surf_display.m
M       cat_surf_vol2surf.m
A       internal/cat_vol_atlas.m
 M      templates_1.50mm

New:     Added internal cat_vol_atlas function to normalize, optimize and merge
         common atlas datasets such as AAL, IBSR, HAMMERS, ANATOMY, MORI, LPBA40,
         Neuromorphometrics,  ...
         The function optimize, normalize and merge the atlas ROIs of one or
         multiple subjects as 4D probability map to create a single 3D atlas map.
         It use CAT preprocessing and median filtering to optimize and normalize
         the individual atlas ROIs and try to rename the ROI names given by the
         CSV Files by a dictionary.
         The function is still in development, the principle idea works, but
         the naming is not correct for all regions.
Changed: Replace SPM PS by MATLAB print function to write CAT report as PDF,
         because the PS is outdated and does not work with surfaces.
Changed: Common print structure in cat_surf_display and cat_main.
Changed: Added SPM command line link for cat_surf_vol2surf output, if job.verb
         is >0.
Fixed:   Corrected surface colormap and scaling after changing to SPM gray.
Fixed:   Double surface output in CAT report.
Fixed:   Changed thickness field estimation and fixed writing in XML file.
Comment: Added ;; in MATLAB code to mark special lines to jump in the editor.


------------------------------------------------------------------------
r807 | dahnke | 2015-12-01 15:10:24 +0100 (Tue, 01 Dec 2015) | 12 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       cat_surf_createCS.m
M       cat_surf_display.m
M       compile.m

(1)  Changed: Updated surface output of CAT report by using cat_surf_display.
(2)  New:     Added new parameters in cat_surf_display for CAT report.
(3)  New:     Added test function for cat_vol_genus0 and cat_vol_interp3f in
              compile function.

------------------------------------------------------------------------
r806 | dahnke | 2015-12-01 10:09:32 +0100 (Tue, 01 Dec 2015) | 9 lines

Changed paths:
 M      .
M       CHANGES.txt
M       cat_main.m
M       cat_run.m
MM      cat_stat_IQR.m

(1)  Fixed: Corrected pbtres parameter handling

------------------------------------------------------------------------
r805 | dahnke | 2015-11-30 18:54:48 +0100 (Mon, 30 Nov 2015) | 33 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_extopts.m
M       cat_io_FreeSurfer.m
M       cat_main.m
M       cat_surf_createCS.m
M       cat_vol_gradient3.c
M       cat_vol_pbt.m
M       compile.m
M       ds.m
M       tbx_cfg_cat.m
D       templates_1.50mm/aal.xml
D       templates_1.50mm/hammers.xml
D       templates_1.50mm/ibsr.xml
A  +    templates_1.50mm/label_dartel_aal.xml
A  +    templates_1.50mm/label_dartel_hammers.xml
A  +    templates_1.50mm/label_dartel_ibsr.xml
A  +    templates_1.50mm/label_dartel_lpba40.xml
A  +    templates_1.50mm/label_dartel_mori.xml
A  +    templates_1.50mm/label_dartel_neuromorphometrics.xml
A  +    templates_1.50mm/lpba40.csv
D       templates_1.50mm/lpba40.xml
D       templates_1.50mm/mori.xml
D       templates_1.50mm/neuromorphometrics.xml

(1)  Changed: Renamed atlas XML files.
(2)  New:     Added lpba40 CSV file.
(3)  New:     Added pbtres in developer GUI.
(4)  Fixed:   Figure handling in private slice display function ds.
(5)  Fixed:   Error in FreeSurfer curvature read function.
(6)  New:     Added further tests in compile function.


------------------------------------------------------------------------
r804 | gaser | 2015-11-30 16:55:44 +0100 (Mon, 30 Nov 2015) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_tools.m
A       cat_stat_IQR.m
M       cat_stat_check_cov.m

(1) New: Added tool to get IQR from xml-files and save it as file.
(2) Fixed: Corrected xml-fields in cat_stat_check_cov.m

------------------------------------------------------------------------
r803 | gaser | 2015-11-30 15:29:15 +0100 (Mon, 30 Nov 2015) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
 M      cross_compiling.txt
M       html/cat.html
M       spm_cat12.m

Fixed: Check for CAT-binaries in spm_cat12.m

------------------------------------------------------------------------
r802 | gaser | 2015-11-30 14:47:16 +0100 (Mon, 30 Nov 2015) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat12.m
M       cat_defaults.m
M       cat_run.m
M       html/cat.html
M       spm_cat12.m

(1) New: Added check whether CAT binaries are running in spm_cat12.m that
    gives system information in case that it fails.
(2) Fixed: Added check of job.nproc filed in cat_run.m.
(3) Fixed: clearvars dows not work on all systems.


------------------------------------------------------------------------
r801 | gaser | 2015-11-29 21:37:10 +0100 (Sun, 29 Nov 2015) | 6 lines

Changed paths:
M       CHANGES.txt
A       cross_compiling.txt

New: Added notes fro cross-compiling.

------------------------------------------------------------------------
r800 | gaser | 2015-11-29 21:32:36 +0100 (Sun, 29 Nov 2015) | 6 lines

Changed paths:
M       CHANGES.txt

(1) Fixed: Again new binaries for linux are now 64bit based on glibc2.12.
(2) Changed: Updated Makefile to allow copy of binaries.

------------------------------------------------------------------------
r799 | gaser | 2015-11-29 21:32:31 +0100 (Sun, 29 Nov 2015) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       html/cat.html

(1) Fixed: Again new binaries for linux are now 64bit based on glibc2.12.
(2) Changed: Updated Makefile to allow copy of binaries.

------------------------------------------------------------------------
r798 | gaser | 2015-11-29 15:31:38 +0100 (Sun, 29 Nov 2015) | 5 lines

Changed paths:
M       CHANGES.txt

Fixed: New binaries for linux are now 64bit based on glibc2.11.

------------------------------------------------------------------------
r797 | gaser | 2015-11-29 15:31:30 +0100 (Sun, 29 Nov 2015) | 8 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       html/cat.html

Fixed: New binaries for linux are now 64bit based on glibc2.11.

------------------------------------------------------------------------
r796 | gaser | 2015-11-27 17:21:31 +0100 (Fri, 27 Nov 2015) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_run.m

Changed: Replaced compiled CAT-files for glnx86 because they needed some
libraries.

------------------------------------------------------------------------
r795 | gaser | 2015-11-27 16:18:10 +0100 (Fri, 27 Nov 2015) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_defaults.m
M       cat_main.m
M       cat_surf_createCS.m
M       html/cat.html

Changed: Set debug option and use debug=2 for saving debugging information
and debug=1 for being more verbose.

------------------------------------------------------------------------
r794 | gaser | 2015-11-27 15:42:35 +0100 (Fri, 27 Nov 2015) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       cat_tst_qa.m
M       html/cat.html

(1) Fixed: Some errors in cat_main regarding expert flag.
(2) Changed: Hardware information using mexext instead of computer.


------------------------------------------------------------------------
r793 | dahnke | 2015-11-27 13:57:03 +0100 (Fri, 27 Nov 2015) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_createCS.m
M       cat_tst_qa.m
M       spm_cat12.m

(1)  Fixed:   Minimal PBT resolution (0.5 > 0.25 mm).
(2)  Fixed:   SPM initialization for fast CAT start.
(3)  Changed: Add hardware information for QA XML file.


------------------------------------------------------------------------
r792 | gaser | 2015-11-27 13:32:32 +0100 (Fri, 27 Nov 2015) | 12 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       cat_surf_createCS.m
M       html/cat.html

(1) Changed: Estimation of gyrus(WM)- and sulcus-width only in expert
    modus 2.
(2) Fixed: Zombie error in cat_main again if surface pipleine fails.


------------------------------------------------------------------------
r791 | gaser | 2015-11-27 11:57:52 +0100 (Fri, 27 Nov 2015) | 9 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_stat_TIV.m
M       html/cat.html

Fixed: Updated xml entries in cat_stat_TIV.m.


------------------------------------------------------------------------
r790 | gaser | 2015-11-27 10:23:54 +0100 (Fri, 27 Nov 2015) | 22 lines

Changed paths:
M       CHANGES.txt
M       cat_amap.mexa64
M       cat_ornlm.mexa64
M       cat_sanlm.mexa64
M       cat_vbdist.mexa64
M       cat_vol_downcut.mexa64
M       cat_vol_eidist.mexa64
M       cat_vol_genus0.mexa64
M       cat_vol_gradient3.mexa64
M       cat_vol_interp3f.mexa64
M       cat_vol_laplace3.mexa64
M       cat_vol_laplace3R.mexa64
M       cat_vol_localstat.mexa64
M       cat_vol_median3.mexa64
M       cat_vol_median3c.mexa64
M       cat_vol_pbtp.mexa64
M       cat_vol_simgrow.mexa64

Changed: Updated linux + mac mex-files.


------------------------------------------------------------------------
r789 | gaser | 2015-11-27 10:19:15 +0100 (Fri, 27 Nov 2015) | 19 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Makefile
M       cat_conf_long.m
M       cat_long_main.m
M       cat_main.m
M       html/cat.html
 M      templates_1.50mm/lpba40.nii
MM      templates_1.50mm/lpba40.txt
 M      templates_1.50mm/lpba40.xml

(1) Fixed: Zombie error in cat_main.m due to crashing surface pipeline
    and wrong catch call to variable "subj".
(2) Fixed: Long. batch was running with background processes.
(3) Changed: Updated linux binaries to 64bit.
(4) Changed: Updated Makefile to also allow copying binaries.
(5) Changed: Removed ROI entry from long. batch mode.

------------------------------------------------------------------------
r788 | gaser | 2015-11-26 17:19:16 +0100 (Thu, 26 Nov 2015) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_run.m

Changed: Removed check of nproc field and check of too many processes
in cat_run.m

------------------------------------------------------------------------
r787 | dahnke | 2015-11-26 16:17:16 +0100 (Thu, 26 Nov 2015) | 20 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_main.m
M       cat_run.m
M       cat_run_newcatch.m
M       cat_stat_marks.m
M       cat_tst_qa.m
M       spm_cat12.m
M       tbx_cfg_cat.m
M       templates_animals/cat_defaults_ape_greater.m
M       templates_animals/cat_defaults_ape_lesser.m
M       templates_animals/cat_defaults_monkey_newworld.m
M       templates_animals/cat_defaults_monkey_oldworld.m

(1)  Fixed:   XML output in error case.
(2)  Changed: Renamed of XML structure and removed unnecessary variables.
(3)  Changed: Update parameter in primate cat_defaults.


------------------------------------------------------------------------
r786 | gaser | 2015-11-26 14:38:40 +0100 (Thu, 26 Nov 2015) | 15 lines

Changed paths:
M       CHANGES.txt
M       cat_defaults.m
M       cat_stat_check_cov.m
M       html/cat_starting.html
M       tbx_cfg_cat.m
M       templates_1.50mm/hammers.xml
A       templates_1.50mm/lpba40.nii
A       templates_1.50mm/lpba40.txt
A       templates_1.50mm/lpba40.xml
M       templates_1.50mm/mori.xml
M       templates_1.50mm/neuromorphometrics.xml

Changed default modulation and updated help and html text accordingly.

------------------------------------------------------------------------
r785 | gaser | 2015-11-26 10:14:24 +0100 (Thu, 26 Nov 2015) | 28 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_long.m
M       cat_batch_vbm.m
M       cat_conf_long.m
M       cat_conf_tools.m
M       cat_io_FreeSurfer.m
M       cat_io_cprintf.m
M       cat_main.m
M       cat_run_job.m
M       cat_stat_TIV.m
M       cat_stat_check_cov.m
M       cat_stat_showslice_all.m
M       cat_stat_spm.m
M       cat_stat_spmF2x.m
M       cat_stat_spmT2x.m
M       cat_surf_createCS.m
M       cat_surf_render.m
M       cat_surf_resamp.m
M       cat_surf_resamp_freesurfer.m
M       cat_vol_slice_overlay.m
M       cat_vol_slice_overlay_ui.m
M       html/cat.html

Used code analyzer to remove many unused variables and corrected code
according to suggestions.

------------------------------------------------------------------------
r784 | gaser | 2015-11-25 16:07:30 +0100 (Wed, 25 Nov 2015) | 12 lines

Changed paths:
M       CAT12-Manual.doc
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       cat_run.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Corrected old vbm_vol_morph call.
(2) Updated multi-threading slightly.

------------------------------------------------------------------------
r783 | dahnke | 2015-11-25 13:20:24 +0100 (Wed, 25 Nov 2015) | 19 lines

Changed paths:
M       CHANGES.txt
M       cat12.m
M       cat_main.m
M       cat_run.m
M       cat_run_job.m
M       cat_vol_partvol.m
M       spm_cat12.m
M       templates_animals/cat_defaults_ape_greater.m
M       templates_animals/cat_defaults_ape_lesser.m
M       templates_animals/cat_defaults_monkey_newworld.m
M       templates_animals/cat_defaults_monkey_oldworld.m

(1)  Cosmetic changes in pseudo multi-threading command line output in cat_run.m
     Call MATLAB with full path (set PATH does not work in every shell).
(2)  Changes in cat_defaults_*primates* parameter files.
(3)  Faster CAT initialization.


------------------------------------------------------------------------
r782 | gaser | 2015-11-25 10:14:42 +0100 (Wed, 25 Nov 2015) | 15 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_main.m
M       cat_run.m
M       cat_run_job.m
M       cat_run_newcatch.m
M       cat_run_oldcatch.m
M       html/cat.html
M       tbx_cfg_cat.m

(1) Removed estwrite option that was not used anymore.
(2) Updated multi-threading slightly.
(3) Many changes to cat_run.m to allow correct output names that are returned.

------------------------------------------------------------------------
r781 | gaser | 2015-11-23 23:43:44 +0100 (Mon, 23 Nov 2015) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_main.m
M       tbx_cfg_cat.m
 M      templates_surfaces/lh.thickness.Template_T1_IXI555_MNI152
 M      templates_surfaces/rh.thickness.Template_T1_IXI555_MNI152

Corrected typo in cat_main for job.cat12.cat12atlas (was job.cat.cat12atlas).

------------------------------------------------------------------------
r780 | gaser | 2015-11-23 16:53:24 +0100 (Mon, 23 Nov 2015) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_run.m
M       spm_cat12.m
M       tbx_cfg_cat.m

Added pseudo multi-threading to cat_run.m


------------------------------------------------------------------------
r779 | gaser | 2015-11-22 21:34:22 +0100 (Sun, 22 Nov 2015) | 17 lines

Changed paths:
M       CHANGES.txt
M       cat12.fig
M       cat12.m
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_stat_TIV.m
M       cat_surf_vol2surf.m
A       templates_surfaces/lh.thickness.Template_T1_IXI555_MNI152
A       templates_surfaces/rh.thickness.Template_T1_IXI555_MNI152

(1) Modified cat_stat_TIV that it runs as batch mode only.
(2) Added button to cat12.m for estimating TIV.
(3) Updated volume to surface mapping. Now absolute boundary as well
    as absolute boundary sampling (range) is provided.


------------------------------------------------------------------------
r778 | gaser | 2015-11-20 11:19:09 +0100 (Fri, 20 Nov 2015) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       cat_batch_vbm.m
M       cat_batch_vbm.sh
MM      cat_stat_TIV.m
M       html/cat.html

Updated batch mode files.


------------------------------------------------------------------------
r777 | gaser | 2015-11-19 16:53:11 +0100 (Thu, 19 Nov 2015) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_conf_stools.m
M       cat_conf_tools.m
M       cat_surf_vol2surf.m
M       cat_tst_qa.m
 M      templates_surfaces/lh.inflated.freesurfer.gii
 M      templates_surfaces/rh.inflated.freesurfer.gii

(1) In cat_surf_vol2surf.m the wrong flag for calling CAT_3DVol2Surf was
    used instead of "avg".
(2) Quality assurance is commented out from cat_conf_tools.m because it
    is not yet ready.
(3) Corrected some field names and removed fields that were not used anymore
    in cat_conf_stools.m.

------------------------------------------------------------------------
r776 | gaser | 2015-11-19 01:19:34 +0100 (Thu, 19 Nov 2015) | 11 lines

Changed paths:
M       CHANGES.txt
M       Contents.m
M       Contents_info.txt
M       cat_conf_tools.m
A       cat_stat_TIV.m
M       html/cat.html

Added and updated functions to read raw volumes and TIV from xml-files.


------------------------------------------------------------------------
r775 | dahnke | 2015-11-18 17:13:57 +0100 (Wed, 18 Nov 2015) | 20 lines

Changed paths:
 M      .
M       CHANGES.txt
A       Contents.m
M       cat12.fig
M       cat12.m
M       html/cat.txt
 M      html/cat_methods_LP.html
M       spm_cat12.m
M       tbx_cfg_cat.m
M       templates_animals/cat_defaults_ape_greater.m
M       templates_animals/cat_defaults_ape_lesser.m
M       templates_animals/cat_defaults_monkey_newworld.m
M       templates_animals/cat_defaults_monkey_oldworld.m

(1)  Corrected problems for simple call of "cat12.m".
(2)  If only CAT is running and no SPM Menu figure is active, all figures (also
     Interactive and Graphics) will be closed.
(3)  Deactivate resizing of cat12 menu.

------------------------------------------------------------------------
r774 | gaser | 2015-11-18 16:53:05 +0100 (Wed, 18 Nov 2015) | 20 lines

Changed paths:
M       CHANGES.txt
M       Contents_info.txt
M       Makefile
M       cat12.fig
M       cat_check.m
M       cat_main.m
M       cat_update.m
M       html/cat.html
D       templates_1.50mm/p0A.nii
D       templates_surfaces/lh.inflated.Template_T1_IXI555_MNI152.gii
A       templates_surfaces/lh.inflated.freesurfer.gii
D       templates_surfaces/rh.inflated.Template_T1_IXI555_MNI152.gii
A       templates_surfaces/rh.inflated.freesurfer.gii

(1) Replaced ?h.inflated.Template_T1_IXI555_MNI152.gii by inflated
    surfaces of fsaverage from freesurfer
(2) Updated Contents.m file
(3) Some smaller rather cosmetic changes.

------------------------------------------------------------------------
r773 | dahnke | 2015-11-18 13:18:08 +0100 (Wed, 18 Nov 2015) | 30 lines

Changed paths:
 M      .
M       CHANGES.txt
M       cat12.m
D       cat_defaults_template_humanIXI555.m
D       cat_set_defaults.m
 M      html
M       html/CAT.png
M       html/cat.html
A       html/cat_methods_LP.html
M       html/style.css
M       spm_cat12.m
D       templates_animals/ape_greater_cg_vbm_defaults.m
D       templates_animals/ape_lesser_cg_vbm_defaults.m
A  +    templates_animals/cat_defaults_ape_greater.m
A       templates_animals/cat_defaults_ape_lesser.m
A       templates_animals/cat_defaults_monkey_newworld.m
A       templates_animals/cat_defaults_monkey_oldworld.m
D       templates_animals/cg_vbm_defaults_template_primate130.m
D       templates_animals/cg_vbm_defaults_template_primate15.m
D       templates_animals/cg_vbm_defaults_template_primate400.m
D       templates_animals/cg_vbm_defaults_template_primate45.m
D       templates_animals/monkey_newworld_cg_vbm_defaults.m
D       templates_animals/monkey_oldworld_cg_vbm_defaults.m

(1)  Extension of "spm_cat12" to use this function as VBM12 GUI starter with
     separate default input file. Hence "cat_set_defaults" is obsolete.
(2)  Remove old animal default files and add new one.


------------------------------------------------------------------------
r772 | gaser | 2015-11-18 12:02:01 +0100 (Wed, 18 Nov 2015) | 57 lines

Changed paths:
M       CHANGES.txt
A  +    cat_amap.c
A  +    cat_amap.m
A  +    cat_amap.mexa64
A  +    cat_amap.mexglx
A  +    cat_amap.mexmaci64
A  +    cat_amap.mexw32
A  +    cat_amap.mexw64
M       cat_main.m
D       cat_mex_amap.c
D       cat_mex_amap.m
D       cat_mex_amap.mexa64
D       cat_mex_amap.mexglx
D       cat_mex_amap.mexmaci64
D       cat_mex_amap.mexw32
D       cat_mex_amap.mexw64
D       cat_mex_ornlm.c
D       cat_mex_ornlm.m
D       cat_mex_ornlm.mexa64
D       cat_mex_ornlm.mexglx
D       cat_mex_ornlm.mexmaci
D       cat_mex_ornlm.mexmaci64
D       cat_mex_ornlm.mexw32
D       cat_mex_ornlm.mexw64
D       cat_mex_sanlm.c
D       cat_mex_sanlm.m
D       cat_mex_sanlm.mexa64
D       cat_mex_sanlm.mexglx
D       cat_mex_sanlm.mexmaci64
D       cat_mex_sanlm.mexw32
D       cat_mex_sanlm.mexw64
A  +    cat_ornlm.c
A  +    cat_ornlm.m
A  +    cat_ornlm.mexa64
A  +    cat_ornlm.mexglx
A  +    cat_ornlm.mexmaci
A  +    cat_ornlm.mexmaci64
A  +    cat_ornlm.mexw32
A  +    cat_ornlm.mexw64
M       cat_run_job.m
A  +    cat_sanlm.c
A  +    cat_sanlm.m
A  +    cat_sanlm.mexa64
A  +    cat_sanlm.mexglx
A  +    cat_sanlm.mexmaci64
A  +    cat_sanlm.mexw32
A  +    cat_sanlm.mexw64
M       cat_vol_isarnlm.m
M       cat_vol_sanlm.m
M       compile.m
M       html/cat.html

Removed _mex from mex-files because this is not consistent with other
mex-functions and other names will interfere with gui-functions such
as cat_vol_sanlm.m

------------------------------------------------------------------------
r771 | gaser | 2015-11-18 11:54:01 +0100 (Wed, 18 Nov 2015) | 72 lines

Changed paths:
M       CHANGES.txt
R  +    Makefile
D       Makefile.cat
D       Makefile.var
D       cat_amap_mex.c
D       cat_amap_mex.m
D       cat_amap_mex.mexa64
D       cat_amap_mex.mexglx
D       cat_amap_mex.mexmaci64
D       cat_amap_mex.mexw32
D       cat_amap_mex.mexw64
M       cat_main.m
A  +    cat_mex_amap.c
A  +    cat_mex_amap.m
A  +    cat_mex_amap.mexa64
A  +    cat_mex_amap.mexglx
A  +    cat_mex_amap.mexmaci64
A  +    cat_mex_amap.mexw32
A  +    cat_mex_amap.mexw64
A  +    cat_mex_ornlm.c
A  +    cat_mex_ornlm.m
A  +    cat_mex_ornlm.mexa64
A  +    cat_mex_ornlm.mexglx
A  +    cat_mex_ornlm.mexmaci
A  +    cat_mex_ornlm.mexmaci64
A  +    cat_mex_ornlm.mexw32
A  +    cat_mex_ornlm.mexw64
A  +    cat_mex_sanlm.c
A  +    cat_mex_sanlm.m
A  +    cat_mex_sanlm.mexa64
A  +    cat_mex_sanlm.mexglx
A  +    cat_mex_sanlm.mexmaci64
A  +    cat_mex_sanlm.mexw32
A  +    cat_mex_sanlm.mexw64
D       cat_ornlm_mex.c
D       cat_ornlm_mex.m
D       cat_ornlm_mex.mexa64
D       cat_ornlm_mex.mexglx
D       cat_ornlm_mex.mexmaci
D       cat_ornlm_mex.mexmaci64
D       cat_ornlm_mex.mexw32
D       cat_ornlm_mex.mexw64
M       cat_run_job.m
D       cat_sanlm_mex.c
D       cat_sanlm_mex.m
D       cat_sanlm_mex.mexa64
D       cat_sanlm_mex.mexglx
D       cat_sanlm_mex.mexmaci64
D       cat_sanlm_mex.mexw32
D       cat_sanlm_mex.mexw64
M       cat_vbdist.mexmaci64
M       cat_vol_downcut.mexmaci64
M       cat_vol_eidist.mexmaci64
M       cat_vol_genus0.mexmaci64
M       cat_vol_gradient3.mexmaci64
M       cat_vol_interp3f.mexmaci64
M       cat_vol_isarnlm.m
M       cat_vol_laplace3.mexmaci64
M       cat_vol_laplace3R.mexmaci64
M       cat_vol_localstat.mexmaci64
M       cat_vol_median3.mexmaci64
M       cat_vol_median3c.mexmaci64
M       cat_vol_pbtp.mexmaci64
M       cat_vol_sanlm.m
M       cat_vol_simgrow.mexmaci64
M       compile.m

(1) Removed Makefile.var and renamed Makefile.cat to Makefile because all
    the compilation is done inside compile.m
(2) Renamed mex-files according to cat_mex_name.*.

------------------------------------------------------------------------
r770 | gaser | 2015-11-18 11:20:03 +0100 (Wed, 18 Nov 2015) | 13 lines

Changed paths:
M       CHANGES.txt
M       INSTALL_info.txt
A  +    cat_defaults_template_humanIXI555.m
D       cg_vbm_defaults_template_humanIXI555.m
M       html/cat.html
M       html/cat_starting.html
D       human_IXI555_cg_vbm_defaults.m

Renamed and updated cat_defaults_template_humanIXI555.m and removed
old human_IXI555_cg_vbm_defaults.m.


------------------------------------------------------------------------
r769 | gaser | 2015-11-18 00:06:11 +0100 (Wed, 18 Nov 2015) | 21 lines

Changed paths:
M       CHANGES.txt
M       Makefile.cat
M       cat_batch_long.m
M       cat_batch_long.sh
M       cat_batch_vbm.m
A  +    cat_conf_long.m
M       cat_conf_tools.m
D       cat_long_multi.m
M       cat_stat_check_cov.m
M       cat_vol_defs.m
M       html/cat.html
M       html/cat.txt
M       html/cat_instruction_FN.html
M       html/cat_instruction_PP.html
M       html/cat_methods_RBM.html

(1) Again renaming of vbm-names that were overseen before.
(2) Updated longitudinal batch that was not working from shell.


------------------------------------------------------------------------
r768 | gaser | 2015-11-17 17:14:11 +0100 (Tue, 17 Nov 2015) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_batch_long.m
M       cat_batch_vbm.m
M       cat_long_main.m

Renamed some cat2-names in cat.

------------------------------------------------------------------------
r767 | gaser | 2015-11-17 17:00:13 +0100 (Tue, 17 Nov 2015) | 34 lines

Changed paths:
M       CHANGES.txt
M       cat12.fig
M       cat12.m
M       cat_batch_long.m
M       cat_batch_spm.m
M       cat_batch_vbm.m
M       cat_check.m
M       cat_defaults.m
M       cat_get_defaults.m
M       cat_io_checkinopt.m
M       cat_io_csv.m
M       cat_io_xml.m
M       cat_io_xml2csv.m
M       cat_long_main.m
M       cat_main.m
M       cat_plot_boxplot.m
M       cat_run.m
M       cat_run_job.m
M       cat_stat_marks.m
M       cat_surf_calc.m
M       cat_surf_createCS.m
M       cat_surf_display.m
M       cat_tst_calc_kappa.m
M       cat_vol_approx.m
M       cat_vol_atlas.m
M       cat_vol_isarnlm.m
M       cat_vol_pbt.m
M       cg_vbm_defaults_template_humanIXI555.m
M       human_IXI555_cg_vbm_defaults.m

Again a lot of more renaming.


------------------------------------------------------------------------
r766 | gaser | 2015-11-17 16:05:32 +0100 (Tue, 17 Nov 2015) | 116 lines

Changed paths:
D       AmapMex.c
D       AmapMex.m
D       AmapMex.mexa64
D       AmapMex.mexglx
D       AmapMex.mexmaci64
D       AmapMex.mexw32
D       AmapMex.mexw64
A  +    CAT12-Manual.doc
A  +    CAT12-Manual.pdf
M       CHANGES.txt
M       Contents_info.txt
M       INSTALL_info.txt
M       Makefile
M       Makefile.cat
D       VBM12-Manual.doc
D       VBM12-Manual.pdf
M       cat12.fig
A  +    cat_amap_mex.c
A  +    cat_amap_mex.m
A  +    cat_amap_mex.mexa64
A  +    cat_amap_mex.mexglx
A  +    cat_amap_mex.mexmaci64
A  +    cat_amap_mex.mexw32
A  +    cat_amap_mex.mexw64
M       cat_batch_long.m
M       cat_batch_spm.m
D       cat_cfg_extopts.m
D       cat_cfg_opts.m
D       cat_cfg_stools.m
D       cat_cfg_stoolsexp.m
D       cat_cfg_tools.m
A  +    cat_conf_extopts.m
A  +    cat_conf_opts.m
A  +    cat_conf_stools.m
A  +    cat_conf_stoolsexp.m
A  +    cat_conf_tools.m
A  +    cat_debug.m
M       cat_io_writenii.m
A  +    cat_long_main.m
M       cat_long_multi.m
M       cat_long_multi_run.m
M       cat_main.m
A  +    cat_ornlm_mex.c
A  +    cat_ornlm_mex.m
A  +    cat_ornlm_mex.mexa64
A  +    cat_ornlm_mex.mexglx
A  +    cat_ornlm_mex.mexmaci
A  +    cat_ornlm_mex.mexmaci64
A  +    cat_ornlm_mex.mexw32
A  +    cat_ornlm_mex.mexw64
M       cat_run_job.m
A  +    cat_sanlm_mex.c
A  +    cat_sanlm_mex.m
A  +    cat_sanlm_mex.mexa64
A  +    cat_sanlm_mex.mexglx
A  +    cat_sanlm_mex.mexmaci64
A  +    cat_sanlm_mex.mexw32
A  +    cat_sanlm_mex.mexw64
M       cat_vol_atlas.m
A  +    cat_vol_defs.m
M       cat_vol_isarnlm.m
M       cat_vol_sanlm.m
M       cat_vol_slice_overlay_ui.m
D       cg_cfg_realign.m
D       cg_cleanup_gwc.m
D       cg_debug.m
D       cg_lat_index.m
D       cg_long_main.m
D       cg_morph_vol.m
D       cg_noise_estimation.m
D       cg_realign.m
D       cg_run_realign_estimate.m
D       cg_run_realign_estwrite.m
D       cg_vbm_bias.m
D       cg_vbm_bias_run.m
D       cg_vbm_brainmask.m
D       cg_vbm_brainmask_ui.m
D       cg_vol_defs.m
M       compile.m
M       html/cat.html
D       ornlmMex.c
D       ornlmMex.m
D       ornlmMex.mexa64
D       ornlmMex.mexglx
D       ornlmMex.mexmaci
D       ornlmMex.mexmaci64
D       ornlmMex.mexw32
D       ornlmMex.mexw64
D       sanlmMex.c
D       sanlmMex.m
D       sanlmMex.mexa64
D       sanlmMex.mexglx
D       sanlmMex.mexmaci64
D       sanlmMex.mexw32
D       sanlmMex.mexw64
M       spm_cat12.m
M       tbx_cfg_cat.m
M       templates_1.50mm/aal.txt
M       templates_1.50mm/anatomy.txt
M       templates_1.50mm/hammers.txt
M       templates_1.50mm/ibsr.txt
M       templates_1.50mm/mori.txt
M       templates_1.50mm/neuromorphometrics.txt
M       templates_animals/ape_greater_cg_vbm_defaults.m
M       templates_animals/ape_lesser_cg_vbm_defaults.m
M       templates_animals/cg_vbm_defaults_template_primate130.m
M       templates_animals/cg_vbm_defaults_template_primate15.m
M       templates_animals/cg_vbm_defaults_template_primate400.m
M       templates_animals/cg_vbm_defaults_template_primate45.m
M       templates_animals/monkey_newworld_cg_vbm_defaults.m
M       templates_animals/monkey_oldworld_cg_vbm_defaults.m

(1) Again a lot of more renaming.
(2) Updating of cat12.fig to consider new functions.

------------------------------------------------------------------------
r765 | gaser | 2015-11-17 14:32:00 +0100 (Tue, 17 Nov 2015) | 42 lines

Changed paths:
!       AmapMex.mexmaci64
M       CHANGES.txt
A  +    Makefile.cat
D       Makefile.vbm
M       cat_io_writenii.m
M       cat_main.m
M       cat_run_job.m
M       cat_surf_createCS.m
A  +    cat_vbdist.c
A  +    cat_vbdist.mexa64
A  +    cat_vbdist.mexglx
A  +    cat_vbdist.mexmaci64
A  +    cat_vbdist.mexw32
A  +    cat_vbdist.mexw64
M       cat_vol_approx.m
M       cat_vol_atlas.m
M       cat_vol_iscale.m
M       cat_vol_morph.m
M       cat_vol_partvol.m
M       cat_vol_pbt.m
M       cat_vol_resize.m
M       cg_morph_vol.m
M       compile.m
D       cshift3D.m
D       diffeo3d.c
D       diffeo3d.h
D       spm_def2det.c
D       spm_def2det.mexa64
D       spm_def2det.mexglx
D       spm_def2det.mexmaci64
D       spm_def2det.mexw32
D       spm_def2det.mexw64
D       vbdist.c
D       vbdist.mexa64
D       vbdist.mexglx
D       vbdist.mexmaci64
D       vbdist.mexw32
D       vbdist.mexw64

Huge renaming from vbm to cat.

------------------------------------------------------------------------
r764 | gaser | 2015-11-17 14:11:53 +0100 (Tue, 17 Nov 2015) | 396 lines

Changed paths:
M       CHANGES.txt
M       Contents_info.txt
A  +    cat12.fig
A  +    cat12.m
A  +    cat_batch_long.m
A  +    cat_batch_long.sh
A  +    cat_batch_spm.m
A  +    cat_batch_spm.sh
A  +    cat_batch_vbm.m
A  +    cat_batch_vbm.sh
A  +    cat_cfg_extopts.m
A  +    cat_cfg_opts.m
A  +    cat_cfg_stools.m
A  +    cat_cfg_stoolsexp.m
A  +    cat_cfg_tools.m
A  +    cat_check.m
A  +    cat_check_system_output.m
A  +    cat_defaults.m
A  +    cat_get_defaults.m
A  +    cat_io_3Dto4D.m
A  +    cat_io_FreeSurfer.m
A  +    cat_io_cgw2seg.m
A  +    cat_io_checkinopt.m
A  +    cat_io_cmd.m
A  +    cat_io_colormaps.m
A  +    cat_io_cprintf.m
A  +    cat_io_csv.m
A  +    cat_io_handle_pre.m
A  +    cat_io_img2nii.m
A  +    cat_io_matlabversion.m
A  +    cat_io_remat.m
A  +    cat_io_seg2cgw.m
A  +    cat_io_struct2table.m
A  +    cat_io_updateStruct.m
A  +    cat_io_writenii.m
A  +    cat_io_xml.m
A  +    cat_io_xml2csv.m
A  +    cat_long_multi.m
A  +    cat_long_multi_run.m
A  +    cat_main.m
A  +    cat_plot_boxplot.m
A  +    cat_run.m
A  +    cat_run_job.m
A  +    cat_run_newcatch.m
A  +    cat_run_oldcatch.m
A  +    cat_set_defaults.m
A  +    cat_stat_calc_stc.m
A  +    cat_stat_check_cov.m
A  +    cat_stat_marks.m
A  +    cat_stat_nanmean.m
A  +    cat_stat_nanmedian.m
A  +    cat_stat_nanstat1d.m
A  +    cat_stat_nanstd.m
A  +    cat_stat_nansum.m
A  +    cat_stat_showslice_all.m
A  +    cat_stat_spm.m
A  +    cat_stat_spmF2x.m
A  +    cat_stat_spmT2x.m
A  +    cat_surf_avg.m
A  +    cat_surf_calc.m
A  +    cat_surf_createCS.m
A  +    cat_surf_display.m
A  +    cat_surf_info.m
A  +    cat_surf_parameters.m
A  +    cat_surf_rename.m
A  +    cat_surf_render.m
A  +    cat_surf_resamp.m
A  +    cat_surf_resamp_freesurfer.m
A  +    cat_surf_resample.m
A  +    cat_surf_smooth.m
A  +    cat_surf_vol2surf.m
A  +    cat_tst_BWPsliceartifact.m
A  +    cat_tst_CJV.m
A  +    cat_tst_calc_kappa.m
A  +    cat_tst_qa.m
A  +    cat_tst_staple_multilabels.m
A  +    cat_update.m
A  +    cat_vol_ROIval.c
A  +    cat_vol_ROIval.mexmaci64
A  +    cat_vol_approx.m
A  +    cat_vol_atlas.m
A  +    cat_vol_average.m
A  +    cat_vol_calc_roi.m
A  +    cat_vol_correct_slice_scaling.m
A  +    cat_vol_ctype.m
A  +    cat_vol_downcut.c
A  +    cat_vol_downcut.mexa64
A  +    cat_vol_downcut.mexglx
A  +    cat_vol_downcut.mexmaci64
A  +    cat_vol_downcut.mexw32
A  +    cat_vol_downcut.mexw64
A  +    cat_vol_eidist.c
A  +    cat_vol_eidist.mexa64
A  +    cat_vol_eidist.mexglx
A  +    cat_vol_eidist.mexmaci64
A  +    cat_vol_eidist.mexw32
A  +    cat_vol_eidist.mexw64
A  +    cat_vol_eikonal3.c
A  +    cat_vol_eikonal3.mexa64
A  +    cat_vol_eikonal3.mexglx
A  +    cat_vol_eikonal3.mexmaci64
A  +    cat_vol_eikonal3.mexw32
A  +    cat_vol_eikonal3.mexw64
A  +    cat_vol_findfiles.m
A  +    cat_vol_genus0.c
A  +    cat_vol_genus0.mexa64
A  +    cat_vol_genus0.mexglx
A  +    cat_vol_genus0.mexmaci64
A  +    cat_vol_genus0.mexw32
A  +    cat_vol_genus0.mexw64
A  +    cat_vol_gradient3.c
A  +    cat_vol_gradient3.mexa64
A  +    cat_vol_gradient3.mexglx
A  +    cat_vol_gradient3.mexmaci64
A  +    cat_vol_gradient3.mexw32
A  +    cat_vol_gradient3.mexw64
A  +    cat_vol_groupwise_ls.m
A  +    cat_vol_imcalc.m
A  +    cat_vol_interp3f.cpp
A  +    cat_vol_interp3f.mexa64
A  +    cat_vol_interp3f.mexglx
A  +    cat_vol_interp3f.mexmaci64
A  +    cat_vol_interp3f.mexw32
A  +    cat_vol_interp3f.mexw64
A  +    cat_vol_isarnlm.m
A  +    cat_vol_iscale.m
A  +    cat_vol_laplace3.c
A  +    cat_vol_laplace3.mexa64
A  +    cat_vol_laplace3.mexglx
A  +    cat_vol_laplace3.mexmaci64
A  +    cat_vol_laplace3.mexw32
A  +    cat_vol_laplace3.mexw64
A  +    cat_vol_laplace3R.c
A  +    cat_vol_laplace3R.mexa64
A  +    cat_vol_laplace3R.mexglx
A  +    cat_vol_laplace3R.mexmaci64
A  +    cat_vol_laplace3R.mexw32
A  +    cat_vol_laplace3R.mexw64
A  +    cat_vol_localstat.c
A  +    cat_vol_localstat.mexa64
A  +    cat_vol_localstat.mexglx
A  +    cat_vol_localstat.mexmaci64
A  +    cat_vol_localstat.mexw32
A  +    cat_vol_localstat.mexw64
A  +    cat_vol_median3.c
A  +    cat_vol_median3.mexa64
A  +    cat_vol_median3.mexglx
A  +    cat_vol_median3.mexmaci64
A  +    cat_vol_median3.mexw32
A  +    cat_vol_median3.mexw64
A  +    cat_vol_median3c.c
A  +    cat_vol_median3c.mexa64
A  +    cat_vol_median3c.mexglx
A  +    cat_vol_median3c.mexmaci64
A  +    cat_vol_median3c.mexw32
A  +    cat_vol_median3c.mexw64
A  +    cat_vol_morph.m
A  +    cat_vol_nanmean3.m
A  +    cat_vol_partvol.m
A  +    cat_vol_pbt.m
A  +    cat_vol_pbtp.cpp
A  +    cat_vol_pbtp.mexa64
A  +    cat_vol_pbtp.mexglx
A  +    cat_vol_pbtp.mexmaci64
A  +    cat_vol_pbtp.mexw32
A  +    cat_vol_pbtp.mexw64
A  +    cat_vol_resize.m
A  +    cat_vol_sanlm.m
A  +    cat_vol_series_align.m
A  +    cat_vol_set_com.m
A  +    cat_vol_simgrow.c
A  +    cat_vol_simgrow.mexa64
A  +    cat_vol_simgrow.mexglx
A  +    cat_vol_simgrow.mexmaci64
A  +    cat_vol_simgrow.mexw32
A  +    cat_vol_simgrow.mexw64
A  +    cat_vol_slice_overlay.m
A  +    cat_vol_slice_overlay_ui.m
A  +    cat_vol_smooth3X.m
D       cg_calculate_volume_ROI.m
M       cg_cfg_realign.m
D       cg_check_cov.m
A  +    cg_debug.m
A  +    cg_long_main.m
M       cg_realign.m
D       cg_set_com.m
D       cg_showslice_all.m
D       cg_slice_overlay.m
D       cg_slice_overlay_ui.m
D       cg_spmF2x.m
D       cg_spmT2x.m
D       cg_spm_batch.m
D       cg_spm_batch.sh
D       cg_vbm_batch.m
D       cg_vbm_batch.sh
M       cg_vbm_bias.m
M       cg_vbm_bias_run.m
M       cg_vbm_brainmask.m
M       cg_vbm_brainmask_ui.m
D       cg_vbm_debug.m
D       cg_vbm_defaults.m
M       cg_vbm_defaults_template_humanIXI555.m
D       cg_vbm_defs.m
D       cg_vbm_extopts.m
D       cg_vbm_get_defaults.m
D       cg_vbm_longitudinal.m
D       cg_vbm_longitudinal_batch.m
D       cg_vbm_longitudinal_batch.sh
D       cg_vbm_longitudinal_multi.m
D       cg_vbm_longitudinal_multi_run.m
D       cg_vbm_opts.m
D       cg_vbm_run.m
D       cg_vbm_run_job.m
D       cg_vbm_run_newcatch.m
D       cg_vbm_run_oldcatch.m
D       cg_vbm_stools.m
D       cg_vbm_stoolsexp.m
D       cg_vbm_tools.m
D       cg_vbm_update.m
D       cg_vbm_write.m
A  +    cg_vol_defs.m
D       checkinopt.m
M       compile.m
M       distribute_to_server.sh
M       ds.m
D       histeq_mask.nii
D       histeq_mask.txt
M       html/cat.html
M       html/cat_FAQ.html
M       html/cat_instruction_FF.html
M       html/cat_instruction_FN.html
M       html/cat_instruction_MS.html
M       html/cat_instruction_PP.html
M       html/cat_instruction_QA.html
M       html/cat_instruction_templates.html
M       html/cat_methods_RBM.html
M       html/cat_starting.html
M       human_IXI555_cg_vbm_defaults.m
A  +    spm_cat12.m
D       spm_vbm12.m
A  +    tbx_cfg_cat.m
D       tbx_cfg_vbm.m
A  +    templates_1.50mm/cat12.nii
D       templates_1.50mm/vbm12.nii
D       vbm12.fig
D       vbm12.m
D       vbm12.man
D       vbm_check.m
D       vbm_check_system_output.m
D       vbm_findfiles.m
D       vbm_io_3Dto4D.m
D       vbm_io_FreeSurfer.m
D       vbm_io_cgw2seg.m
D       vbm_io_cmd.m
D       vbm_io_colormaps.m
D       vbm_io_cprintf.m
D       vbm_io_csv.m
D       vbm_io_handle_pre.m
D       vbm_io_img2nii.m
D       vbm_io_matlabversion.m
D       vbm_io_remat.m
D       vbm_io_seg2cgw.m
D       vbm_io_struct2table.m
D       vbm_io_updateStruct.m
D       vbm_io_writenii.m
D       vbm_io_xml.m
D       vbm_io_xml2csv.m
D       vbm_plot_boxplot.m
D       vbm_qa_calcSTC.m
D       vbm_set_cg_vbm_defaults.m
D       vbm_spm.m
D       vbm_stat_marks.m
D       vbm_stat_nanmean.m
D       vbm_stat_nanmedian.m
D       vbm_stat_nanstat1d.m
D       vbm_stat_nanstd.m
D       vbm_stat_nansum.m
D       vbm_surf_avg.m
D       vbm_surf_calc.m
D       vbm_surf_createCS.m
D       vbm_surf_display.m
D       vbm_surf_info.m
D       vbm_surf_parameters.m
D       vbm_surf_rename.m
D       vbm_surf_render.m
D       vbm_surf_resamp.m
D       vbm_surf_resamp_freesurfer.m
D       vbm_surf_resample.m
D       vbm_surf_smooth.m
D       vbm_surf_vol2surf.m
D       vbm_tst_BWPsliceartifact.m
D       vbm_tst_CJV.m
D       vbm_tst_calc_kappa.m
D       vbm_tst_qa.m
D       vbm_tst_staple_multilabels.m
D       vbm_vol_ROIval.c
D       vbm_vol_ROIval.mexmaci64
D       vbm_vol_approx.m
D       vbm_vol_atlas.m
D       vbm_vol_average.m
D       vbm_vol_correct_slice_scaling.m
D       vbm_vol_ctype.m
D       vbm_vol_downcut.c
D       vbm_vol_downcut.mexa64
D       vbm_vol_downcut.mexglx
D       vbm_vol_downcut.mexmaci64
D       vbm_vol_downcut.mexw32
D       vbm_vol_downcut.mexw64
D       vbm_vol_eidist.c
D       vbm_vol_eidist.mexa64
D       vbm_vol_eidist.mexglx
D       vbm_vol_eidist.mexmaci64
D       vbm_vol_eidist.mexw32
D       vbm_vol_eidist.mexw64
D       vbm_vol_eikonal3.c
D       vbm_vol_eikonal3.mexa64
D       vbm_vol_eikonal3.mexglx
D       vbm_vol_eikonal3.mexmaci64
D       vbm_vol_eikonal3.mexw32
D       vbm_vol_eikonal3.mexw64
D       vbm_vol_genus0.c
D       vbm_vol_genus0.mexa64
D       vbm_vol_genus0.mexglx
D       vbm_vol_genus0.mexmaci64
D       vbm_vol_genus0.mexw32
D       vbm_vol_genus0.mexw64
D       vbm_vol_gradient3.c
D       vbm_vol_gradient3.mexa64
D       vbm_vol_gradient3.mexglx
D       vbm_vol_gradient3.mexmaci64
D       vbm_vol_gradient3.mexw32
D       vbm_vol_gradient3.mexw64
D       vbm_vol_groupwise_ls.m
D       vbm_vol_imcalc.m
D       vbm_vol_interp3f.cpp
D       vbm_vol_interp3f.mexa64
D       vbm_vol_interp3f.mexglx
D       vbm_vol_interp3f.mexmaci64
D       vbm_vol_interp3f.mexw32
D       vbm_vol_interp3f.mexw64
D       vbm_vol_isarnlm.m
D       vbm_vol_iscale.m
D       vbm_vol_laplace3.c
D       vbm_vol_laplace3.mexa64
D       vbm_vol_laplace3.mexglx
D       vbm_vol_laplace3.mexmaci64
D       vbm_vol_laplace3.mexw32
D       vbm_vol_laplace3.mexw64
D       vbm_vol_laplace3R.c
D       vbm_vol_laplace3R.mexa64
D       vbm_vol_laplace3R.mexglx
D       vbm_vol_laplace3R.mexmaci64
D       vbm_vol_laplace3R.mexw32
D       vbm_vol_laplace3R.mexw64
D       vbm_vol_localstat.c
D       vbm_vol_localstat.mexa64
D       vbm_vol_localstat.mexglx
D       vbm_vol_localstat.mexmaci64
D       vbm_vol_localstat.mexw32
D       vbm_vol_localstat.mexw64
D       vbm_vol_median3.c
D       vbm_vol_median3.mexa64
D       vbm_vol_median3.mexglx
D       vbm_vol_median3.mexmaci64
D       vbm_vol_median3.mexw32
D       vbm_vol_median3.mexw64
D       vbm_vol_median3c.c
D       vbm_vol_median3c.mexa64
D       vbm_vol_median3c.mexglx
D       vbm_vol_median3c.mexmaci64
D       vbm_vol_median3c.mexw32
D       vbm_vol_median3c.mexw64
D       vbm_vol_morph.m
D       vbm_vol_nanmean3.m
D       vbm_vol_partvol.m
D       vbm_vol_pbt.m
D       vbm_vol_pbtp.cpp
D       vbm_vol_pbtp.mexa64
D       vbm_vol_pbtp.mexglx
D       vbm_vol_pbtp.mexmaci64
D       vbm_vol_pbtp.mexw32
D       vbm_vol_pbtp.mexw64
D       vbm_vol_resize.m
D       vbm_vol_sanlm.m
D       vbm_vol_series_align.m
D       vbm_vol_simgrow.c
D       vbm_vol_simgrow.mexa64
D       vbm_vol_simgrow.mexglx
D       vbm_vol_simgrow.mexmaci64
D       vbm_vol_simgrow.mexw32
D       vbm_vol_simgrow.mexw64
D       vbm_vol_smooth3X.m

Huge renaming from vbm to cat.

------------------------------------------------------------------------
r763 | gaser | 2015-11-17 12:32:31 +0100 (Tue, 17 Nov 2015) | 13 lines

Changed paths:
M       CHANGES.txt
M       cg_vbm_defs.m
M       cg_vbm_run_job.m
M       html/CAT.png
M       vbm_io_writenii.m
M       vbm_tst_qa.m

(1) Use old modulation throughout VBM12. Changed a lot of according
    code in vbm_io_writenii.m and cg_vbm_defs.m.
(2) Some smaller cosmetic changes and typo correction.
(3) release number of VBM12 was not correctly estimated in vbm_tst_qa.m.

------------------------------------------------------------------------
r762 | gaser | 2015-11-13 13:56:23 +0100 (Fri, 13 Nov 2015) | 12 lines

Changed paths:
M       CHANGES.txt
M       cg_vbm_longitudinal.m
M       cg_vbm_run.m
M       cg_vbm_run_job.m
M       cg_vbm_write.m
M       checkinopt.m
M       tbx_cfg_vbm.m

(1) Updated some fields for longitudinal pipeline.
(2) Some smaller cosmetic changes and typo minimization.

------------------------------------------------------------------------
r761 | gaser | 2015-11-12 00:47:35 +0100 (Thu, 12 Nov 2015) | 12 lines

Changed paths:
M       CHANGES.txt
M       cg_vbm_defs.m
M       cg_vbm_run.m
M       cg_vbm_run_job.m
M       cg_vbm_write.m

(1) cg_vbm_write.m saved the deformation from the SPM registration
    and not from the dartel registration (now use trans.warped.y rather
    than trans.atlas.Yy).
(2) Some smaller changes to help textes or names.

------------------------------------------------------------------------
r760 | gaser | 2015-11-11 21:11:28 +0100 (Wed, 11 Nov 2015) | 19 lines

Changed paths:
M       CHANGES.txt
M       Makefile.vbm
M       cg_cfg_realign.m
M       cg_run_realign_estimate.m
M       cg_run_realign_estwrite.m
M       cg_vbm_defaults.m
M       cg_vbm_defs.m
M       cg_vbm_extopts.m
M       cg_vbm_run_job.m
 M      html/CAT.png
M       tbx_cfg_vbm.m
M       vbm_surf_render.m

(1) Removed some typos in several files.
(2) Removed wrong warp option in tbx_cfg_vbm.m.
(3) Set expertgui option to 0 in cg_vbm_default.m.


------------------------------------------------------------------------
r759 | dahnke | 2015-11-09 10:38:54 +0100 (Mon, 09 Nov 2015) | 28 lines

Changed paths:
M       CHANGES.txt
M       cg_vbm_defaults.m
M       cg_vbm_extopts.m
M       cg_vbm_run.m
M       cg_vbm_run_job.m
M       cg_vbm_run_newcatch.m
M       cg_vbm_run_oldcatch.m
M       cg_vbm_write.m
M       ds.m
M       tbx_cfg_vbm.m
M       vbm_vol_isarnlm.m
M       vbm_vol_partvol.m

(1)  Dartel resolution limit as minimum voxel size only in best resolution case.
(2)  Set millimeter-based boxing rather in voxel-based for brain boundary box.
(3)  Changes in the cg_vbm_defaults output definition. Replaced affine entry by
     dartel entry.
(4)  Added ISARNLM (Iterative Spatial Adaptive multi-Resolution Non Local Means)
     filter for high resolution data (<0.7 mm) to deal better with noise in
     interpolation, parallel-imaging and band-width artifacts.
(5)  Updated APP processing and options. Corrected problems of data with strong
     bias (7T) or/and large ventricle (IXI175).
(6)  Added cls 4-6 output for template generation.
(7)  Corrected using of SPM class values (minimum fraction has to be 10%).
(8)  Corrected command line output.
(9)  Unready optimizations of the WMH correction.

------------------------------------------------------------------------
r758 | gaser | 2015-10-28 15:41:21 +0100 (Wed, 28 Oct 2015) | 10 lines

Changed paths:
M       CHANGES.txt
M       cg_check_cov.m
M       vbm_vol_pbt.m

(1) Removed some typos in vbm_vol_pbt.m.
(2) Handling and shortening of filenames in cg_check_cov.m is now done
    sample-wise.


------------------------------------------------------------------------
r757 | gaser | 2015-10-27 08:20:49 +0100 (Tue, 27 Oct 2015) | 55 lines

Changed paths:
M       CHANGES.txt
M       Makefile.vbm
M       cg_check_cov.m
M       cg_vbm_extopts.m
A       html/CAT.png
A  +    html/cat.html
A  +    html/cat.txt
A  +    html/cat_FAQ.html
A  +    html/cat_ackknowledgement.html
A  +    html/cat_instruction.html
A  +    html/cat_instruction_FF.html
A  +    html/cat_instruction_FN.html
A  +    html/cat_instruction_MS.html
A  +    html/cat_instruction_PP.html
A  +    html/cat_instruction_QA.html
A  +    html/cat_instruction_ST.html
A  +    html/cat_instruction_templates.html
A  +    html/cat_introduction.html
A  +    html/cat_methods.html
A  +    html/cat_methods_QA.html
A  +    html/cat_methods_RBM.html
A  +    html/cat_methods_SBM.html
A  +    html/cat_methods_VBM.html
A  +    html/cat_starting.html
A  +    html/cat_stuff.html
D       html/vbm12.html
D       html/vbm12.txt
D       html/vbm12_FAQ.html
D       html/vbm12_ackknowledgement.html
D       html/vbm12_instruction.html
D       html/vbm12_instruction_FF.html
D       html/vbm12_instruction_FN.html
D       html/vbm12_instruction_MS.html
D       html/vbm12_instruction_PP.html
D       html/vbm12_instruction_QA.html
D       html/vbm12_instruction_ST.html
D       html/vbm12_instruction_templates.html
D       html/vbm12_introduction.html
D       html/vbm12_methods.html
D       html/vbm12_methods_QA.html
D       html/vbm12_methods_RBM.html
D       html/vbm12_methods_SBM.html
D       html/vbm12_methods_VBM.html
D       html/vbm12_starting.html
D       html/vbm12_stuff.html
 M      sliderPanel.m
M       spm_vbm12.m
M       vbm12.fig
M       vbm12.m

(1) Rename VBM to CAT in html-code and added new logo.
(2) Slightly changed vbm12.figure according to new names.
(3) Changed position of buttons and colorbar in cg_check_cov.m.

------------------------------------------------------------------------
r756 | dahnke | 2015-10-20 18:30:50 +0200 (Tue, 20 Oct 2015) | 25 lines

Changed paths:
M       CHANGES.txt
M       cg_vbm_batch.m
M       cg_vbm_defaults.m
M       cg_vbm_extopts.m
M       cg_vbm_run_job.m
M       cg_vbm_write.m
M       ds.m
M       vbm_surf_display.m
M       vbm_surf_resamp.m
M       vbm_vol_partvol.m

(1)  Added affine preprocessing (APP=Affine PreProcessing) in cg_vbm_run_job
     with APP parameter in cg_vbm_defaults and experimental expert GUI option.
     APP include a bias rough bias correction and brain extraction to support
     untypical cases (non-human/neonates) with registration problems.
     This also include changes in preprocessing 1 part in the cg_vbm_write.
(2)  Removed high resolution voxel size limit.
(3)  Corrected tiny error that ignored rigid data output parameter.
(4)  Deactivate divergence variable in LAS and set lower upper threshold for GM
     because of problems in high contrast data with strong GM variation where
     low GM intensities were not corrected and therefore misclassified as CSF.
     Further tiny changes to stabilize the CSF/background field.
(5)  Improved segmentation of subcortical regions in vbm_vol_partvol.

------------------------------------------------------------------------
r755 | gaser | 2015-10-19 07:41:58 +0200 (Mon, 19 Oct 2015) | 7 lines

Changed paths:
M       CHANGES.txt
M       vbm_surf_createCS.m

Some cosmetic changes to vbm_surf_createCS.m.


------------------------------------------------------------------------
r754 | gaser | 2015-10-18 23:37:27 +0200 (Sun, 18 Oct 2015) | 10 lines

Changed paths:
M       CHANGES.txt
D       Contents.m

Added sliderPanel.m.





------------------------------------------------------------------------
r753 | gaser | 2015-10-18 23:37:04 +0200 (Sun, 18 Oct 2015) | 12 lines

Changed paths:
M       CHANGES.txt
A       Contents.m
M       html/vbm12.html
A       sliderPanel.m

Added sliderPanel.m.





------------------------------------------------------------------------
r752 | gaser | 2015-10-18 21:24:02 +0200 (Sun, 18 Oct 2015) | 49 lines

Changed paths:
M       AmapMex.mexw32
M       AmapMex.mexw64
M       CHANGES.txt
M       html/vbm12.html
M       ornlmMex.mexw32
M       ornlmMex.mexw64
M       sanlmMex.mexw32
M       sanlmMex.mexw64
M       templates_1.50mm/neuromorphometrics.csv
M       vbdist.mexw32
M       vbdist.mexw64
M       vbm_vol_downcut.mexw32
M       vbm_vol_downcut.mexw64
M       vbm_vol_eidist.c
M       vbm_vol_eidist.mexa64
M       vbm_vol_eidist.mexglx
M       vbm_vol_eidist.mexmaci64
M       vbm_vol_eidist.mexw32
M       vbm_vol_eidist.mexw64
M       vbm_vol_genus0.mexw32
M       vbm_vol_genus0.mexw64
M       vbm_vol_gradient3.mexw32
M       vbm_vol_gradient3.mexw64
M       vbm_vol_interp3f.mexw32
M       vbm_vol_interp3f.mexw64
M       vbm_vol_laplace3.mexw32
M       vbm_vol_laplace3.mexw64
M       vbm_vol_laplace3R.mexw32
M       vbm_vol_laplace3R.mexw64
M       vbm_vol_localstat.mexw32
M       vbm_vol_localstat.mexw64
M       vbm_vol_median3.mexw32
M       vbm_vol_median3.mexw64
M       vbm_vol_median3c.mexw32
M       vbm_vol_median3c.mexw64
M       vbm_vol_pbtp.mexw32
M       vbm_vol_pbtp.mexw64
M       vbm_vol_simgrow.mexw32
M       vbm_vol_simgrow.mexw64


(1) Recompiled code.
(2) Corrected doubled definition in vbm_vol_eidist.c.





------------------------------------------------------------------------
r751 | gaser | 2015-10-18 20:47:01 +0200 (Sun, 18 Oct 2015) | 10 lines

Changed paths:
M       CHANGES.txt
M       vbm_vol_eidist.c
M       vbm_vol_eidist.mexmaci64

(1) Many cosmetic changes to vbm_vol_eidist.c.
(2) Removed maci64-bug in vbm_vol_eidist.c.



------------------------------------------------------------------------
r750 | gaser | 2015-10-13 13:39:39 +0200 (Tue, 13 Oct 2015) | 32 lines

Changed paths:
M       CHANGES.txt
M       cg_check_cov.m
M       html/vbm12.html
M       html/vbm12.txt
M       html/vbm12_FAQ.html
M       html/vbm12_ackknowledgement.html
M       html/vbm12_instruction.html
M       html/vbm12_instruction_FF.html
M       html/vbm12_instruction_FN.html
M       html/vbm12_instruction_MS.html
M       html/vbm12_instruction_PP.html
M       html/vbm12_instruction_QA.html
M       html/vbm12_instruction_ST.html
M       html/vbm12_instruction_templates.html
M       html/vbm12_introduction.html
M       html/vbm12_methods.html
M       html/vbm12_methods_QA.html
M       html/vbm12_methods_RBM.html
M       html/vbm12_methods_SBM.html
M       html/vbm12_methods_VBM.html
M       html/vbm12_starting.html
M       html/vbm12_stuff.html
M       vbm12.fig

(1) Changed y-limit in cg_check_cov.m.
(2) Updated html-files with many changes and additional links.





------------------------------------------------------------------------
r749 | gaser | 2015-10-09 18:04:18 +0200 (Fri, 09 Oct 2015) | 21 lines

Changed paths:
M       AmapMex.mexw64
M       CHANGES.txt
M       ornlmMex.mexw64
M       sanlmMex.mexw64
M       vbdist.mexw64
M       vbm_vol_downcut.mexw64
M       vbm_vol_eidist.mexw64
M       vbm_vol_genus0.mexw64
M       vbm_vol_gradient3.mexw64
M       vbm_vol_interp3f.mexw64
M       vbm_vol_laplace3.mexw64
M       vbm_vol_laplace3R.mexw64
M       vbm_vol_localstat.mexw64
M       vbm_vol_median3.mexw64
M       vbm_vol_median3c.mexw64
M       vbm_vol_pbtp.mexw64
M       vbm_vol_simgrow.mexw64

Recompiled windows 64bit.

------------------------------------------------------------------------
r748 | gaser | 2015-10-09 17:04:18 +0200 (Fri, 09 Oct 2015) | 7 lines

Changed paths:
M       CHANGES.txt
M       svn_ci_log

Tiny change in svn_ci_log


------------------------------------------------------------------------
r747 | gaser | 2015-10-09 17:02:55 +0200 (Fri, 09 Oct 2015) | 6 lines

Changed paths:
M       CHANGES.txt

Tiny change in svn_ci_log


------------------------------------------------------------------------
r746 | gaser | 2015-10-09 17:02:04 +0200 (Fri, 09 Oct 2015) | 7 lines

Changed paths:
M       CHANGES.txt
M       svn_ci_log

Tiny change in svn_ci_log


------------------------------------------------------------------------
r745 | gaser | 2015-10-09 16:58:04 +0200 (Fri, 09 Oct 2015) | 84 lines

Changed paths:
M       Amap.c
M       AmapMex.mexa64
M       AmapMex.mexglx
M       AmapMex.mexmaci64
M       AmapMex.mexw32
M       AmapMex.mexw64
M       CHANGES.txt
M       Kmeans.c
M       Makefile.vbm
M       MrfPrior.c
M       cg_vbm_defaults.m
M       cg_vbm_run_job.m
M       cg_vbm_write.m
M       compile.m
M       genus0.c
M       html/vbm12.html
M       ornlmMex.mexmaci64
M       ornlmMex.mexw32
M       ornlmMex.mexw64
M       sanlmMex.mexa64
M       sanlmMex.mexglx
M       sanlmMex.mexmaci64
M       sanlmMex.mexw32
M       sanlmMex.mexw64
D       sanlmMex_noopenmp.mexa64
D       sanlmMex_noopenmp.mexglx
D       sanlmMex_noopenmp.mexmaci64
D       sanlmMex_noopenmp.mexw32
D       sanlmMex_noopenmp.mexw64
M       sanlm_float.c
M       vbdist.c
M       vbdist.mexa64
M       vbdist.mexglx
M       vbdist.mexmaci64
M       vbdist.mexw32
M       vbdist.mexw64
M       vbm_vol_downcut.mexmaci64
M       vbm_vol_downcut.mexw32
M       vbm_vol_downcut.mexw64
M       vbm_vol_eidist.mexmaci64
M       vbm_vol_eidist.mexw32
M       vbm_vol_eidist.mexw64
M       vbm_vol_genus0.mexa64
M       vbm_vol_genus0.mexglx
M       vbm_vol_genus0.mexmaci64
M       vbm_vol_genus0.mexw32
M       vbm_vol_genus0.mexw64
M       vbm_vol_gradient3.mexmaci64
M       vbm_vol_gradient3.mexw32
M       vbm_vol_gradient3.mexw64
M       vbm_vol_interp3f.mexmaci64
M       vbm_vol_interp3f.mexw32
M       vbm_vol_interp3f.mexw64
M       vbm_vol_isarnlm.m
M       vbm_vol_laplace3.mexmaci64
M       vbm_vol_laplace3.mexw32
M       vbm_vol_laplace3.mexw64
M       vbm_vol_laplace3R.mexmaci64
M       vbm_vol_laplace3R.mexw32
M       vbm_vol_laplace3R.mexw64
M       vbm_vol_localstat.mexmaci64
M       vbm_vol_localstat.mexw32
M       vbm_vol_localstat.mexw64
M       vbm_vol_median3.mexmaci64
M       vbm_vol_median3.mexw32
M       vbm_vol_median3.mexw64
M       vbm_vol_median3c.mexmaci64
M       vbm_vol_median3c.mexw32
M       vbm_vol_median3c.mexw64
M       vbm_vol_pbtp.mexmaci64
M       vbm_vol_pbtp.mexw32
M       vbm_vol_pbtp.mexw64
M       vbm_vol_sanlm.m
M       vbm_vol_simgrow.mexmaci64
M       vbm_vol_simgrow.mexw32
M       vbm_vol_simgrow.mexw64

(1) Replaced OPENMP with Posix Threads in sanlm-code for multi-threading.
(2) Use always multithreading SANLM.
(3) Added inclusion of mex.h if mex-file is detected (important for printf
    under fucking windows).
(4) Recompiled everything...

------------------------------------------------------------------------
r744 | gaser | 2015-10-08 14:10:37 +0200 (Thu, 08 Oct 2015) | 8 lines

Changed paths:
M       CHANGES.txt
M       svn_ci_log

Corrected previous changes in svn_ci_log to also include actual
changes.


------------------------------------------------------------------------
r743 | gaser | 2015-10-08 14:10:01 +0200 (Thu, 08 Oct 2015) | 8 lines

Changed paths:
M       CHANGES.txt
M       svn_ci_log

Corrected previous changes in svn_ci_log to also include actual
changes.


------------------------------------------------------------------------
r742 | gaser | 2015-10-08 14:03:13 +0200 (Thu, 08 Oct 2015) | 12 lines

Changed paths:
M       CHANGES.txt
M       html/vbm12_methods_VBM.html
M       svn_ci_log
M       vbm_surf_createCS.m

(1) Added option to deform corrected surface to its uncorrected version
    in aeras where topology correction was made in vbm_surf_createCS.m.
(2) Somed edits in html of VBM method.
(3) Updated svn_ci_log to automatically print all logs > r440 to CHANGES.txt.


------------------------------------------------------------------------
r741 | dahnke | 2015-10-07 20:23:28 +0200 (Wed, 07 Oct 2015) | 21 lines

Changed paths:
M       cg_vbm_batch.m
M       cg_vbm_run_job.m
M       cg_vbm_run_newcatch.m
M       cg_vbm_run_oldcatch.m
M       cg_vbm_write.m
M       vbm_surf_calc.m
M       vbm_surf_display.m
M       vbm_tst_qa.m

(1)  Added command line output of the resulting file in "vbm_surf_calc".
(2)  Replace temporary image output for VBM report by "V.dat" field in
     "cg_vbm_write".
(3)  Added preprocessing parameter (job,res) output in "vbm_tst_qa".
(4)  Added output of the "vbm_*xml" with preprocessing parameter (job) and
     vbmerr, if "cg_vbm_run_job" failed (Changes is "cg_vbm_run_[new|old]catch").
(5)  Small corrections in "cg_vbm_batch".
(6)  Cleaned old primate processing commands in "cg_vbm_run_job".
(7)  ROI estimation only if file exist.


------------------------------------------------------------------------
r740 | dahnke | 2015-10-02 15:38:09 +0200 (Fri, 02 Oct 2015) | 24 lines

Changed paths:
M       cg_vbm_batch.m
M       cg_vbm_extopts.m
M       cg_vbm_run_job.m
M       cg_vbm_write.m
 M      templates_animals
M       vbm_io_writenii.m
M       vbm_surf_display.m
M       vbm_vol_correct_slice_scaling.m

(1)  Updated hard masking of T1 images for non human preprocessing. Although it
     worked with SPM version 6080 by using a brain mask for spm_preproc8, it
     didn't work anymore and a real masking of the T1 data is required. Because
     the masked image is also used for SPM Preprocessing (1 and 2) a relatively
     good skull-stripping (inclusive fast bias correction) was added.
(2)  Added error message in "cg_vbm_batch".
(3)  Updated command window output of "vbm_surf_display".
(4)  Corrected small GUI-error in "vbm_vol_slice_scaling".
(5)  Prepared update of modulated output in "vbm_io_writenii".
(6)  Corrected template setting in "cg_vbm_write". Remove "do_dartel==0" message
     because there is no GUI dartel control option anymore. Added some test
     parameter for Shooting e.g. to reduce the number of iteration.


------------------------------------------------------------------------
r739 | gaser | 2015-10-01 12:00:57 +0200 (Thu, 01 Oct 2015) | 8 lines

Changed paths:
M       cg_vbm_batch.m
M       cg_vbm_write.m

(1) Some small changes in cg_vbm_write regarding batch mode and incorrect
    settings (ROI, LAS).
(2) Corrected ROI setting in cg_vbm_batch.m

------------------------------------------------------------------------
r738 | gaser | 2015-09-28 09:18:10 +0200 (Mon, 28 Sep 2015) | 10 lines

Changed paths:
 M      templates_1.50mm/Template_0_NKI174_MNI152_GS.nii
 M      templates_1.50mm/Template_1_NKI174_MNI152_GS.nii
 M      templates_1.50mm/Template_2_NKI174_MNI152_GS.nii
 M      templates_1.50mm/Template_3_NKI174_MNI152_GS.nii
 M      templates_1.50mm/Template_4_NKI174_MNI152_GS.nii
M       vbm_surf_createCS.m

Undo changes to write pp1-map per default in vbm_surf_createCS.m.

------------------------------------------------------------------------
r737 | gaser | 2015-09-25 17:22:02 +0200 (Fri, 25 Sep 2015) | 16 lines

Changed paths:
M       cg_vbm_batch.m
M       cg_vbm_batch.sh
M       cg_vbm_extopts.m
M       cg_vbm_stools.m
M       cg_vbm_write.m
M       vbm_surf_createCS.m
M       vbm_surf_vol2surf.m

(1) Corrected use of boundary position in vbm_vol_vol2surf.m and cg_vbm_stools.m.
(2) Quote type corrected in cg_vbm_extopts.m.
(3) Added forground flag to cg_vbm_batch.sh for vbmweb use.
(4) Corrected missing output.ROI filed in cg_vbm_write.m.
(5) Write pp1-map per default in vbm_surf_createCS.m for mapping and added
    side information.

------------------------------------------------------------------------
r736 | dahnke | 2015-09-24 17:06:13 +0200 (Thu, 24 Sep 2015) | 23 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_extopts.m
M       cg_vbm_write.m
M       tbx_cfg_vbm.m
 M      templates_1.50mm
A       templates_1.50mm/Template_0_NKI174_MNI152_GS.nii
A       templates_1.50mm/Template_1_NKI174_MNI152_GS.nii
A       templates_1.50mm/Template_2_NKI174_MNI152_GS.nii
A       templates_1.50mm/Template_3_NKI174_MNI152_GS.nii
A       templates_1.50mm/Template_4_NKI174_MNI152_GS.nii
M       vbm_surf_display.m

(1)  Added preliminary Shooting deformation that still requires a correction of
     the affine component of the modulated output with/without - in other words
     the w0r* wr* images are not correct!
     The differentiation between Dartel and Shooting is done by the selected
     template.
(2)  Removed ROI data extraction option from GUI.
(3)  Corrected small errors.
(4)  Corrected another uint8 NAN error.
(5)  Added preliminary Shooting template (Template_*_NKI174_MNI152_GS.nii).

------------------------------------------------------------------------
r735 | gaser | 2015-09-24 10:23:54 +0200 (Thu, 24 Sep 2015) | 7 lines

Changed paths:
M       cg_vbm_write.m
M       tbx_cfg_vbm.m

(1) Added CSF and label again to GUI...
(2) Slightly changed printed outpput of cg_vbm_write.m.

------------------------------------------------------------------------
r734 | dahnke | 2015-09-21 07:57:08 +0200 (Mon, 21 Sep 2015) | 9 lines

Changed paths:
M       CHANGES.txt
M       cg_vbm_write.m
M       vbm_io_writenii.m

Corrected mat0 in rigid output images.



------------------------------------------------------------------------
r733 | gaser | 2015-09-17 13:33:56 +0200 (Thu, 17 Sep 2015) | 7 lines

Changed paths:
M       html/vbm12.html
M       vbm_vol_groupwise_ls.m

Replace noise estimation of NaN by average value in vbm_vol_groupwise_ls.m.


------------------------------------------------------------------------
r732 | gaser | 2015-09-17 10:01:49 +0200 (Thu, 17 Sep 2015) | 14 lines

Changed paths:
M       CHANGES.txt
M       cg_vbm_longitudinal.m
M       cg_vbm_longitudinal_multi.m
M       cg_vbm_longitudinal_multi_run.m
M       html/vbm12.html
M       vbm_vol_groupwise_ls.m
M       vbm_vol_series_align.m

Reorganized and updated longitudinal batch that caused problems with
column cellstr. Thanks to Yang Ding for pointing to that issue.



------------------------------------------------------------------------
r731 | dahnke | 2015-09-16 15:50:24 +0200 (Wed, 16 Sep 2015) | 10 lines

Changed paths:
M       cg_vbm_write.m
M       vbm_tst_qa.m

(1)  Simplification of SPM classification correction and correction of data
     type errors.
(2)  Removed "Subject Averageness" mark, corrected relative volume unit
     (% rather than cm3), and refined quality mark description.


------------------------------------------------------------------------
r730 | gaser | 2015-09-16 11:34:40 +0200 (Wed, 16 Sep 2015) | 12 lines

Changed paths:
M       cg_vbm_batch.sh
M       cg_vbm_tools.m
M       cg_vbm_write.m
M       vbm_vol_groupwise_ls.m
M       vbm_vol_sanlm.m
M       vbm_vol_series_align.m

(1) Removed vbm-dir option in cg_vbm_batch.sh and updated help test.
(2) Some cosmetic changes to cg_vbm_write.m, vbm_vol_sanlm.m
    vbm_vol_groupwise_ls.m, and cg_vbm_tools.m

------------------------------------------------------------------------
r729 | gaser | 2015-09-14 15:44:32 +0200 (Mon, 14 Sep 2015) | 8 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_stools.m

(1) Added expert modus 2 for experimental functions.
(2) Changed some file selection settings according to expert modus.


------------------------------------------------------------------------
r728 | gaser | 2015-09-14 15:28:58 +0200 (Mon, 14 Sep 2015) | 20 lines

Changed paths:
A  +    templates_surfaces/lh.central.freesurfer.gii
D       templates_surfaces/lh.central.gii
A  +    templates_surfaces/lh.sphere.freesurfer.gii
D       templates_surfaces/lh.sphere.gii
A  +    templates_surfaces/rh.central.freesurfer.gii
D       templates_surfaces/rh.central.gii
A  +    templates_surfaces/rh.sphere.freesurfer.gii
D       templates_surfaces/rh.sphere.gii
M       vbm_spm.m
M       vbm_surf_avg.m
M       vbm_surf_createCS.m
M       vbm_surf_resamp.m
M       vbm_surf_resamp_freesurfer.m
M       vbm_surf_resample.m

Renamed ?h.sphere.gii and ?h.central.gii to ?h.central.freesurfer.gii
and ?h.sphere.freesurfer.gii and changed resp. files.


------------------------------------------------------------------------
r727 | gaser | 2015-09-14 14:55:36 +0200 (Mon, 14 Sep 2015) | 11 lines

Changed paths:
M       cg_vbm_opts.m
M       cg_vbm_run.m
M       cg_vbm_write.m
M       tbx_cfg_vbm.m

(1) Removed options for SPM12 bias correction form GUI.
(2) Adapted some fucntions according to (1).
(3) pause(rand) did not work properly, now always pause(1) is used in
    cg_vbm_write.m

------------------------------------------------------------------------
r726 | gaser | 2015-09-14 11:16:14 +0200 (Mon, 14 Sep 2015) | 6 lines

Changed paths:
M       cg_vbm_stools.m

Disabled mapping in native space in  cg_vbm_stools.m. because it is not yet
working because of coordination issues.

------------------------------------------------------------------------
r725 | gaser | 2015-09-14 11:12:05 +0200 (Mon, 14 Sep 2015) | 5 lines

Changed paths:
M       cg_vbm_stools.m

Shortened some names in cg_vbm_stools.m.

------------------------------------------------------------------------
r724 | gaser | 2015-09-14 11:05:36 +0200 (Mon, 14 Sep 2015) | 8 lines

Changed paths:
M       cg_vbm_stools.m
M       vbm_surf_vol2surf.m

(1) Recompiled CAT_3dVol2Surf.c to enable sampling at only one defined position.
(2) Some cosmetic changes to cg_vbm_stools.m and commented out functions that
    are not yet finished.

------------------------------------------------------------------------
r723 | gaser | 2015-09-11 18:11:06 +0200 (Fri, 11 Sep 2015) | 7 lines

Changed paths:
M       cg_vbm_longitudinal.m
M       tbx_cfg_vbm.m

Some cosmetic changes to cg_vbm_longitudinal.m and tbx_cfg_vbm.m.


------------------------------------------------------------------------
r722 | gaser | 2015-09-11 17:36:26 +0200 (Fri, 11 Sep 2015) | 17 lines

Changed paths:
M       cg_vbm_longitudinal.m
M       cg_vbm_longitudinal_multi.m
M       cg_vbm_stools.m
M       cg_vbm_tools.m
M       vbm12.fig
M       vbm_io_xml.m
M       vbm_surf_vol2surf.m

(1) Some cosmetic changes to vbm_surf_vol2surf.m and vbm_io_xml.m
    and cg_vbm_longitudinal_multi.
(2) Renamed longitudinal batch to prevent confucion with spm12 tool for
    longitudinal registration.
(3) Changed and corrected some ufilters in cg_vbm_stools.m.
(4) Changed cg_vbm_longitudinal.m accoring to (3).


------------------------------------------------------------------------
r721 | gaser | 2015-09-10 14:50:23 +0200 (Thu, 10 Sep 2015) | 7 lines

Changed paths:
M       cg_vbm_write.m
M       html/vbm12.html

Corrected bug in cg_vbm_write.m whwre relative volume was not correctly printed.


------------------------------------------------------------------------
r720 | gaser | 2015-09-07 15:46:09 +0200 (Mon, 07 Sep 2015) | 5 lines

Changed paths:
M       cg_vbm_write.m

Corrected bug in cg_vbm_write.m if strength of NLM-filter was set to 0.

------------------------------------------------------------------------
r719 | gaser | 2015-09-07 15:38:03 +0200 (Mon, 07 Sep 2015) | 18 lines

Changed paths:
M       cg_vbm_tools.m
D       templates_surfaces/lh.central.freesurfer.gii
A  +    templates_surfaces/lh.inflated.Template_T1_IXI555_MNI152.gii
D       templates_surfaces/lh.inflated.gii
D       templates_surfaces/lh.s1template.IXI555.gii
D       templates_surfaces/lh.s32template.IXI555.gii
D       templates_surfaces/rh.central.freesurfer.gii
A  +    templates_surfaces/rh.inflated.Template_T1_IXI555_MNI152.gii
D       templates_surfaces/rh.inflated.gii
D       templates_surfaces/rh.s1template.IXI555.gii
D       templates_surfaces/rh.s32template.IXI555.gii

(1) Removed templates_surfaces/?h.central.freesurfer.gii and
    templates_surfaces/?h.s1template.IXI555.gii.
(2) Renamed templates_surfaces/?h.s32template.IXI555.gii to
    templates_surfaces/?h.inflated.Template_T1_IXI555_MNI152.gii

------------------------------------------------------------------------
r718 | gaser | 2015-09-07 15:15:44 +0200 (Mon, 07 Sep 2015) | 17 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_run_job.m
M       cg_vbm_stools.m
M       cg_vbm_stoolsexp.m
M       cg_vbm_tools.m
M       cg_vbm_write.m
M       vbm_surf_createCS.m

(1) Corrected some typos in cg_vbm_defaults.m and vbm_surf_createCS.m.
(2) Updated help text in cg_vbm_tools.m, cg_vbm_stoolsexp.m,
    cg_vbm_stools.m, and cg_vbm_run_job.m
(3) Updated output in cg_vbm_write.m.
(4) Volumes are now printed in black in cg_vbm_write.m.



------------------------------------------------------------------------
r717 | gaser | 2015-09-07 09:10:01 +0200 (Mon, 07 Sep 2015) | 16 lines

Changed paths:
M       cg_vbm_batch.m
M       cg_vbm_defaults.m
M       cg_vbm_extopts.m
M       cg_vbm_opts.m
M       cg_vbm_run.m
M       tbx_cfg_vbm.m

(1) Updated help text for many options in tbx_cfg_vbm.m, cg_vbm_opts.m, and
    cg_vbm_extopts.m.
(2) Removed some options (CSF, label) from GUI.
(3) Updated cg_vbm_run.m and cg_vbm_batch.m according to changes in (2).
(4) Updated expert options in cg_vbm_extopts.m.
(5) Updated some options in cg_vbm_defaults.m-


------------------------------------------------------------------------
r716 | gaser | 2015-09-07 08:58:19 +0200 (Mon, 07 Sep 2015) | 5 lines

Changed paths:
M       cg_vbm_longitudinal_multi.m

Updated help text for modulation in cg_vbm_longitudinal_multi.m

------------------------------------------------------------------------
r715 | gaser | 2015-09-07 08:56:36 +0200 (Mon, 07 Sep 2015) | 8 lines

Changed paths:
M       cg_vbm_stools.m
M       vbm12.fig

(1) Many changes of text and names in cg_vbm_stools.m.
(2) Changed some names in vbm12.fig.


------------------------------------------------------------------------
r714 | gaser | 2015-09-07 08:54:23 +0200 (Mon, 07 Sep 2015) | 10 lines

Changed paths:
M       cg_slice_overlay.m
M       cg_slice_overlay_ui.m

(1) Extended cg_slice_overlay.m by option to automatically display slices
    with local maxima if slice_str is empty string.
(2) Corrected bug in cg_slice_overlay.m for saving images of wrong window.
(3) Updated cg_slice_overlay_ui according to new functions in cg_slice_overlay.m


------------------------------------------------------------------------
r713 | gaser | 2015-09-07 08:49:33 +0200 (Mon, 07 Sep 2015) | 7 lines

Changed paths:
M       cg_check_cov.m
M       html/vbm12.html

Removed bug in cg_check_cov.m fpr MSE estimation for surfaces.


------------------------------------------------------------------------
r712 | gaser | 2015-08-27 16:09:42 +0200 (Thu, 27 Aug 2015) | 7 lines

Changed paths:
M       cg_check_cov.m
M       html/vbm12.html

Added option to sort data according to mean correlation in cg_check_cov.m.


------------------------------------------------------------------------
r711 | gaser | 2015-08-25 15:58:29 +0200 (Tue, 25 Aug 2015) | 17 lines

Changed paths:
M       cg_vbm_batch.m
M       cg_vbm_defaults.m
M       cg_vbm_extopts.m
M       cg_vbm_run_job.m
M       cg_vbm_write.m
M       html/vbm12.html
M       vbm_tst_qa.m
M       vbm_vol_partvol.m

(1) Replaced nanstd by vbm_stat_nanstd in vbm_tst_qa.m.
(2) Updated cg_vbm_batch.m for new default parameters.
(3) Many naming changes to outputs and help texts incg_vbm_write,
    vbm_vol_partvol, cg_vbm_run_job.
(4) Removed error message if peaks are too different in cg_vbm_write.m.


------------------------------------------------------------------------
r710 | gaser | 2015-08-21 17:33:50 +0200 (Fri, 21 Aug 2015) | 6 lines

Changed paths:
M       cg_check_cov.m

Don't use masking anymore in cg_check_cov.m.


------------------------------------------------------------------------
r709 | gaser | 2015-08-21 11:48:49 +0200 (Fri, 21 Aug 2015) | 7 lines

Changed paths:
M       cg_check_cov.m
M       html/vbm12.html

Added estimation of mean squared error to cg_check_cov.m


------------------------------------------------------------------------
r708 | gaser | 2015-08-20 11:02:20 +0200 (Thu, 20 Aug 2015) | 10 lines

Changed paths:
M       cg_showslice_all.m
M       cg_vbm_tools.m
M       html/vbm12.html
M       vbm_surf_render.m
MM      vbm_vol_isarnlm.m

Added option to select slice orientation in cg_showslice_all.m


------------------------------------------------------------------------
r707 | dahnke | 2015-08-17 14:22:10 +0200 (Mon, 17 Aug 2015) | 22 lines

Changed paths:
M       ds.m
M       vbm_stat_marks.m
M       vbm_tst_calc_kappa.m
M       vbm_tst_qa.m

(1)  Added realignment function in "vbm_tst_calc_kappa".
(2)  Major update of the QA estimation "vbm_tst_qa" and "vbm_stat_marks":
     - The last changes (R686-R690) did not show improvements in all test areas.
       There were strong age effects, and only partial improvements that did not
       fit to the increased complexity and run time of the code.
       Therefore, the function was rebuild based on R650 and optimized by the
       best ideas of versions R665-R682 to reduce variation between different
       preprocessing methods (SPM8/12,FSL,VBM8/12) that were a strong problem in
       version R650.
     - Most mentionable is that the focus of noise estimation moved from WM to
       CSF (if possible) to avoid aging effects, where the age depended changes
       of the WM structure can be misinterpreted as noise. Although, the methods
       to avoid these regions work in most cases, some kind of noise/movement
       artifacts showed a similar pattern that lead to an underestimation of
       noise in these cases.

------------------------------------------------------------------------
r706 | dahnke | 2015-08-03 16:40:47 +0200 (Mon, 03 Aug 2015) | 26 lines

Changed paths:
 M      .
M       cg_vbm_defs.m
M       checkinopt.m
M       templates_1.50mm/aal.csv
M       templates_1.50mm/aal.nii
M       templates_1.50mm/aal.txt
M       templates_1.50mm/aal.xml
M       vbm_io_cmd.m
M       vbm_io_updateStruct.m
M       vbm_stat_marks.m
M       vbm_stat_nanmean.m
M       vbm_surf_display.m
M       vbm_vol_atlas.m
M       vbm_vol_average.m
M       vbm_vol_isarnlm.m

(1)  Deactivated "cleanup" case in "vbm_io_cmd", because it did not work in all
     MATLAB versions.
(2)  Restore file data type setting (V.dt, V.pinfo) in "cg_vbm_defs".
(3)  Corrected labeling in AAL atlas.
(4)  Corrected small errors in "vbm_stat_nanmean", "vbm_io_update_Struct",
     "checkinopt"
(5)  Added view options in "vbm_surf_display".


------------------------------------------------------------------------
r705 | gaser | 2015-07-09 10:40:43 +0200 (Thu, 09 Jul 2015) | 9 lines

Changed paths:
M       cg_spmT2x.m
M       cg_vbm_tools.m
M       html/vbm12.html
M       vbm_surf_render.m

(1) Corrected wrong fields in cg_vbm_tools.m and cg_spmT2x.m for thresholds.
(2) Extended vbm_surf_render.m by functions for scaling and png-saving

------------------------------------------------------------------------
r704 | dahnke | 2015-07-07 15:35:05 +0200 (Tue, 07 Jul 2015) | 5 lines

Changed paths:
M       vbm_vol_isarnlm.m

(1)  Corrected small errors in "vbm_vol_isarnlm".

------------------------------------------------------------------------
r703 | dahnke | 2015-07-07 09:10:01 +0200 (Tue, 07 Jul 2015) | 16 lines

Changed paths:
M       cg_vbm_stoolsexp.m
M       ds.m
 M      templates_surfaces
M       vbm_io_writenii.m
M       vbm_stat_marks.m
M       vbm_surf_avg.m
M       vbm_surf_display.m
A       vbm_vol_isarnlm.m
M       vbm_vol_resize.m

(1)  Corrected error in "vbm_surf_display".
(2)  Deactivated mat0 changes in "vbm_io_writenii".
(3)  Added ISARNLM-filter to reduce parallel imaging artifacts.
(4)  Added median reduction in "vbm_vol_resize".

------------------------------------------------------------------------
r702 | gaser | 2015-06-18 17:36:50 +0200 (Thu, 18 Jun 2015) | 7 lines

Changed paths:
M       cg_vbm_write.m
M       html/vbm12.html

Forgot to remove some debugging code in cg_vbm_write.m.


------------------------------------------------------------------------
r701 | gaser | 2015-06-18 17:33:44 +0200 (Thu, 18 Jun 2015) | 9 lines

Changed paths:
M       cg_vbm_run_job.m
M       cg_vbm_write.m
M       html/vbm12.html

(1) In cg_vbm_write.m changed some outputs of the log-page.
(2) Corrected typo in cg_vbm_run_job.m.


------------------------------------------------------------------------
r700 | gaser | 2015-06-17 17:46:39 +0200 (Wed, 17 Jun 2015) | 8 lines

Changed paths:
M       vbm_surf_resample.m
M       vbm_surf_smooth.m

Always overwrite already written data in vbm_surf_resample.m and vbm_surf_smooth.m, otherwise users might
oversee that message if they want to write updated data.


------------------------------------------------------------------------
r699 | gaser | 2015-06-17 17:36:59 +0200 (Wed, 17 Jun 2015) | 8 lines

Changed paths:
M       Makefile.vbm
M       cg_check_cov.m
M       html/vbm12.html

Corrected wrong surface-template folder in cg_check_cov.m.


------------------------------------------------------------------------
r698 | dahnke | 2015-06-02 10:40:10 +0200 (Tue, 02 Jun 2015) | 41 lines

Changed paths:
M       cg_vbm_stools.m
M       cg_vbm_write.m
A       templates_surfaces/lh.central.freesurfer.gii
A       templates_surfaces/rh.central.freesurfer.gii
M       vbm12.fig
M       vbm_surf_calc.m
M       vbm_surf_createCS.m
M       vbm_surf_display.m
M       vbm_surf_info.m
M       vbm_surf_rename.m
M       vbm_surf_render.m
M       vbm_surf_resample.m
M       vbm_surf_smooth.m

(1)  Changes for MT-image processing in "cg_vbm_write":
     - Deactivate SPM MRF filter to 0, because it removed to much informations.
     - Corrected global intensity scaling errors for negative values in MT
       contrast images ("vbm_pre_gintnorm" in "cg_vbm_write").
(2)  LAS updates in "cg_vbm_write":
     - Added estimation for the difference between cortical and subcortical GM
       for further automatic control of the LAS filter strength.
       MT data with lesser variation of GM tissue intensities will have a lower
       CV value and require less adaption.
     - Replaced TPM by Dartel template map.
     - Added divergence skeleton for more better distance based cortical GM
       detection and correction.
(3)  Added a try-catch block for surface creation in "cg_vbm_write".
(4)  Updates for surface rendering:
     - Renamed gyrus and sulcus width surface textures filenames according to
       "thickness" texture filename in "gyruswidth", "gyruswidthWM", and
       "sulcuswidth".
     - Corrected print problems in "vbm_surf_display" (lighting does not work
       with phong) and prepare print function.
     - Set finer colormaps (256 values rather than 32).
     - Added multi-surface display in "vbm_surf_render" and "vbm_surf_display".
(5)  Corrected output directory and progress bar errors in "vbm_surf_calc".
(6)  Added FreeSurfer average surfaces "[lr]h.central.freesurfer.gii".
(7)  Added lazy processing in "vbm_surf_resample" and "vbm_surf_smooth"
     (estimation only if files does not exist).

------------------------------------------------------------------------
r697 | dahnke | 2015-05-18 16:04:03 +0200 (Mon, 18 May 2015) | 14 lines

Changed paths:
M       cg_vbm_extopts.m
M       cg_vbm_run_newcatch.m
M       cg_vbm_run_oldcatch.m
M       cg_vbm_write.m
M       vbm_io_writenii.m
M       vbm_stat_marks.m
M       vbm_surf_createCS.m
M       vbm_surf_display.m
M       vbm_surf_info.m

(1)  Corrected mat0 error in rigide (and affine) output images.
(2)  Added PBT WM and CSF thickness/depth estimation in "vbm_surf_createCS".

------------------------------------------------------------------------
r696 | dahnke | 2015-04-29 14:15:54 +0200 (Wed, 29 Apr 2015) | 10 lines

Changed paths:
M       cg_vbm_stools.m
M       vbm12.fig
M       vbm12.m
M       vbm_surf_display.m
M       vbm_surf_vol2surf.m

(1)  Updated vol2surf GUI.
(2)  Small corrections and updates in "vbm_surf_display".

------------------------------------------------------------------------
r695 | dahnke | 2015-04-27 21:07:15 +0200 (Mon, 27 Apr 2015) | 14 lines

Changed paths:
M       cg_vbm_stools.m
 M      vbm_io_matlabversion.m
MM      vbm_surf_avg.m
M       vbm_surf_info.m
M       vbm_surf_rename.m
MM      vbm_surf_resample.m
A       vbm_surf_vol2surf.m

(1)  Added "vbm_surf_vol2surf" function (alpha) and updated GUI.
     SPM data type (no stepsize correction) and orientation problems
     in "CAT_3dVol2Surf" with subject space data.
(2)  Small corrections in other files.

------------------------------------------------------------------------
r694 | dahnke | 2015-04-24 08:09:23 +0200 (Fri, 24 Apr 2015) | 5 lines

Changed paths:
MM      cg_vbm_stoolsexp.m

(1)

------------------------------------------------------------------------
r693 | dahnke | 2015-04-24 08:08:32 +0200 (Fri, 24 Apr 2015) | 22 lines

Changed paths:
M       cg_vbm_extopts.m
M       cg_vbm_stoolsexp.m
A  +    templates_surfaces/lh.central.Template_T1_IXI555_MNI152.gii
D       templates_surfaces/lh.template.Template_T1_IXI555_MNI152.gii
A  +    templates_surfaces/rh.central.Template_T1_IXI555_MNI152.gii
D       templates_surfaces/rh.template.Template_T1_IXI555_MNI152.gii
M       vbm12.fig
A       vbm_surf_avg.m
M       vbm_surf_display.m
M       vbm_surf_info.m
M       vbm_surf_rename.m
M       vbm_surf_render.m
A       vbm_surf_resample.m
M       vbm_surf_smooth.m

(1)  Added file dependencies for "vbm_surf_smooth".
(2)  Added "vbm_surf_resample" for texture (and surface) resampling.
(3)  Added "vbm_surf_avg" for averaging and smoothing of meshs.
     Mirror averaging of sides did not work correctly.
(4)  Further small corrections.

------------------------------------------------------------------------
r692 | dahnke | 2015-04-23 11:49:12 +0200 (Thu, 23 Apr 2015) | 38 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_extopts.m
M       cg_vbm_stools.m
A       cg_vbm_stoolsexp.m
D       fsaverage
D       fsaverage/fsavg.index2D_256x128.txt
D       fsaverage/lh.central.gii
D       fsaverage/lh.inflated.gii
D       fsaverage/lh.s1template.IXI555.gii
D       fsaverage/lh.s32template.IXI555.gii
D       fsaverage/lh.sphere.gii
D       fsaverage/lh.template.Template_T1_IXI555_MNI152.gii
D       fsaverage/rh.central.gii
D       fsaverage/rh.inflated.gii
D       fsaverage/rh.s1template.IXI555.gii
D       fsaverage/rh.s32template.IXI555.gii
D       fsaverage/rh.sphere.gii
D       fsaverage/rh.template.Template_T1_IXI555_MNI152.gii
M       tbx_cfg_vbm.m
A  +    templates_surfaces
M       vbm12.fig
M       vbm12.m
M       vbm_spm.m
M       vbm_surf_calc.m
M       vbm_surf_createCS.m
M       vbm_surf_display.m
M       vbm_surf_resamp.m
M       vbm_surf_resamp_freesurfer.m
M       vbm_surf_smooth.m

(1)  Added "extopts.expertgui" flag to "cg_vbm_defaults" to add further GUI
     options and batch function (default=0).
(2)  Added "cg_vbm_stoolsepx" for further expert batch functions, if
     "extopts.expertgui==0".
(3)  Updated VBM12 GUI.
(4)  Renamed "fsaverage" to "templates_surfaces".

------------------------------------------------------------------------
r691 | gaser | 2015-04-23 10:40:56 +0200 (Thu, 23 Apr 2015) | 9 lines

Changed paths:
M       Makefile.vbm
M       cg_vbm_defaults.m
M       html/vbm12.html
M       vbm_surf_display.m

Corrected some typos or comments.


------------------------------------------------------------------------
r690 | dahnke | 2015-04-22 14:25:36 +0200 (Wed, 22 Apr 2015) | 21 lines

Changed paths:
M       cg_vbm_write.m
M       vbm_io_cmd.m
A       vbm_io_matlabversion.m
M       vbm_io_writenii.m
M       vbm_surf_calc.m
M       vbm_surf_display.m
M       vbm_surf_smooth.m
M       vbm_tst_qa.m
M       vbm_vol_resize.m

(1)  Added modification to change Dartel resolution in "cg_vbm_write" and
     "vbm_io_writenii" by the "cg_vbm_defaults" parameter "extopts.vox".
(2)  Corrected error in mean mesh estimation and process bar in "vbm_surf_calc".
(3)  Changed datatype of intensity normalized output files from single to uint16.
     The images intensity is not displayed correctly in MRIcron for MAC.
(4)  Corrected small errors in "vbm_surf_display", "vbm_surf_smooth".
(5)  Added "vbm_io_matlabversion" to get the year-release number.
(6)  Corrected small MATLAB version depending error in "vbm_io_cmd" output that
     depend further on "vbm_io_cprintf" line 265.

------------------------------------------------------------------------
r689 | dahnke | 2015-04-19 17:37:49 +0200 (Sun, 19 Apr 2015) | 17 lines

Changed paths:
M       cg_vbm_stools.m
A       internal
M       vbm_io_FreeSurfer.m
M       vbm_io_colormaps.m
A       vbm_surf_calc.m
M       vbm_surf_display.m
M       vbm_surf_info.m
M       vbm_surf_render.m
M       vbm_tst_qa.m

(1)  vbm_surf_calc
(2)  Added further texture handling in "vbm_surf_display".




------------------------------------------------------------------------
r688 | dahnke | 2015-04-17 11:25:22 +0200 (Fri, 17 Apr 2015) | 18 lines

Changed paths:
M       cg_vbm_stools.m
M       vbm12.m
M       vbm_io_colormaps.m
M       vbm_stat_marks.m
M       vbm_surf_display.m
M       vbm_surf_info.m
M       vbm_surf_rename.m
M       vbm_surf_render.m
A       vbm_surf_smooth.m
M       vbm_tst_qa.m

(1)  Corrections and updates of surface management and display functions.
(2)  Added "vbm_suf_smooth" for texture smoothing.
(3)  Added colormaps for surfaces textures.
(4)  Temporary, but not final modification of QA noise estimation.


------------------------------------------------------------------------
r687 | dahnke | 2015-04-15 13:41:19 +0200 (Wed, 15 Apr 2015) | 21 lines

Changed paths:
A       cg_vbm_stools.m
M       cg_vbm_tools.m
M       tbx_cfg_vbm.m
M       vbm12.m
A       vbm_surf_display.m
A       vbm_surf_info.m
A       vbm_surf_rename.m
A       vbm_surf_render.m
M       vbm_tst_qa.m

(1)  Added "vbm_surf_render" a modified version of the "spm_mesh_render" with
     "inner light" and "vbm_surf_display" for further texture handling
(2)  Separate volume and surface tools:
     - cg_vbm_tools      .. volume tools
     - cg_vbm_stools     .. surface tools
(3)  Added management surface functions
     - vbm_surf_info     .. extract surface information from filename
     - vbm_surf_rename   .. replace specific parts of surface filenames


------------------------------------------------------------------------
r686 | dahnke | 2015-04-13 19:26:22 +0200 (Mon, 13 Apr 2015) | 18 lines

Changed paths:
 M      fsaverage/lh.s1template.IXI555.gii
 M      fsaverage/lh.s32template.IXI555.gii
 M      fsaverage/lh.template.Template_T1_IXI555_MNI152.gii
 M      fsaverage/rh.s1template.IXI555.gii
 M      fsaverage/rh.s32template.IXI555.gii
 M      fsaverage/rh.template.Template_T1_IXI555_MNI152.gii
M       vbm_tst_qa.m

(1)  Updated QA estimation, because of large differences between different
     segmentations. Added skull-stripping (especially for FSL and SPM) and a
     fast version of the AMAP segmentation to get similar tissue peaks.
(2)  Updated noise and bias estimation and increased accuracy.
(3)  Updated relative volume marks by experimental values (median relative
     volume and its standard deviation of each tissue class based on a mixed
     dataset of healthy control subjects of multiple databases (IXI, NIH, ...).


------------------------------------------------------------------------
r685 | dahnke | 2015-04-13 18:39:40 +0200 (Mon, 13 Apr 2015) | 26 lines

Changed paths:
 M      .
M       cg_showslice_all.m
M       cg_vbm_write.m
A       fsaverage/lh.s1template.IXI555.gii
A       fsaverage/lh.s32template.IXI555.gii
A       fsaverage/lh.template.Template_T1_IXI555_MNI152.gii
A       fsaverage/rh.s1template.IXI555.gii
A       fsaverage/rh.s32template.IXI555.gii
A       fsaverage/rh.template.Template_T1_IXI555_MNI152.gii
 M      templates_1.50mm
M       vbm_io_csv.m
M       vbm_plot_boxplot.m
M       vbm_stat_marks.m
M       vbm_vol_sanlm.m

(1)  Using of MRF filter in "cg_vbm_write" without prior maps, required a simple
     skull-stripping and update of tissue maps before the MRF filtering.
     Therefore, the loading of the bias corrected image was moved before the
     class correction.
(2)  Corrections of the "cg_vbm_write" final affine registration.
(3)  Corrections in the "cg_vbm_write" cleanup routine.
(4)  Corrected small errors in other files.
(5)  Added template surfaces.


------------------------------------------------------------------------
r684 | gaser | 2015-03-16 16:50:21 +0100 (Mon, 16 Mar 2015) | 10 lines

Changed paths:
M       html/vbm12.html

(1) Changed default values back to SPM-defaults in cg_vbm_defaults.m.
(2) Added function prctile to vbm_plot_boxplot.m to get rid of dependency
    from stat toolbox.
(3) Added new functionality to cg_slice_overlay.m to automatically estimate
    cluster peaks and plot resp. slices as default.


------------------------------------------------------------------------
r683 | gaser | 2015-03-16 16:50:08 +0100 (Mon, 16 Mar 2015) | 13 lines

Changed paths:
M       cg_slice_overlay.m
M       cg_vbm_defaults.m
M       html/vbm12.html
M       vbm_plot_boxplot.m

(1) Changed default values back to SPM-defaults in cg_vbm_defaults.m.
(2) Added function prctile to vbm_plot_boxplot.m to get rid of dependency
    from stat toolbox.
(3) Added new functionality to cg_slice_overlay.m to automatically estimate
    cluster peaks and plot resp. slices as default.


------------------------------------------------------------------------
r682 | dahnke | 2015-03-13 10:38:24 +0100 (Fri, 13 Mar 2015) | 6 lines

Changed paths:
M       cg_vbm_write.m
M       vbm_tst_qa.m

(1)  Corrected data type error in "vbm_tst_qa".

------------------------------------------------------------------------
r681 | dahnke | 2015-03-12 14:02:32 +0100 (Thu, 12 Mar 2015) | 17 lines

Changed paths:
M       cg_vbm_write.m
M       vbm_stat_marks.m
M       vbm_tst_qa.m

(1)  Corrected errors in "cg_vbm_write" due to MRF filtering of SPM segmentation
     that requires skull-stripping / cleanup.
(2)  Corrected error in "vbm_tst_qa" for "cg_vbm_write" call.
(3)  Updated inhomogeneity measure ICR/CIR in "vbm_tst_qa" and rating.
     Test showed low correlation between ICR/CIR and preprocessing quality.
     Used a more relaxed scaling (BWP 100 inhomogeneity ~ mark 3.5, worst case
     real data - HR075 and 7Tesla ~ mark 5 to 6).
(4)  Corrected filter strength of the ORNLM filter. Used CNR previous as input,
     but theornlmMEX function requires a SNR value (~CNR*3).



------------------------------------------------------------------------
r680 | gaser | 2015-03-04 16:37:51 +0100 (Wed, 04 Mar 2015) | 13 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_run_job.m
M       cg_vbm_write.m
M       html/vbm12.html

(1) Changed default values back to r674 in cg_vbm_defaults.m.
(2) Use correct estimate of mat file after final affine transformation.
(3) Added check for field before isfield is called in vbm_tst_qa.m.
(4) Removed saving of vbm12_*.mat file because it's not necessary
    anymore.


------------------------------------------------------------------------
r679 | dahnke | 2015-03-04 09:05:32 +0100 (Wed, 04 Mar 2015) | 7 lines

Changed paths:
M       cg_vbm_write.m
 M      vbm_tst_BWPsliceartifact.m

(1)  Corrected Yy output error for low resolution images.
(2)  Corrected error in final Affine segmentation for low resolution images.

------------------------------------------------------------------------
r678 | dahnke | 2015-03-03 11:29:16 +0100 (Tue, 03 Mar 2015) | 12 lines

Changed paths:
M       cg_vbm_run_job.m
M       cg_vbm_write.m
M       vbm_io_cmd.m
M       vbm_vol_partvol.m

(1)  Added final affine registration in "cg_vbm_write" after segmentation.
(2)  Prepared computer depending font size for vbm-report in "cg_vbm_write".
(3)  New shorter command window output if debug==0 with a final removing of the
     gray output of the subroutines.
     (changes in "vbm_io_cmd","vbm_vol_partvol","cg_vbm_write").

------------------------------------------------------------------------
r677 | dahnke | 2015-03-02 14:59:45 +0100 (Mon, 02 Mar 2015) | 20 lines

Changed paths:
MM      cg_vbm_defaults_template_humanIXI555.m
M       cg_vbm_run_job.m
M       cg_vbm_write.m
MM      templates_animals/cg_vbm_defaults_template_primate130.m
MM      templates_animals/cg_vbm_defaults_template_primate15.m
MM      templates_animals/cg_vbm_defaults_template_primate400.m
MM      templates_animals/cg_vbm_defaults_template_primate45.m
M       vbm_io_writenii.m
A       vbm_tst_BWPsliceartifact.m
M       vbm_vol_partvol.m

(1)  Updated blood vessel detection in "vbm_vol_partvol". Use now a smaller
     region for blood vessel detection to avoid defects in the hippocampus.
(2)  Added contrast check in "cg_vbm_run_job" to avoid preprocessing of inverse
     images (T2/PD weighted) if "extopts.INV=0".
(3)  Updated inverse intensity processing in "vbm_pre_intnorm" in "cg_vbm_write".
(4)  Updated modulated output in "vbm_io_write" to reduce artifacts.
(5)  Corrected output behavior in vbm-report.

------------------------------------------------------------------------
r676 | gaser | 2015-02-26 16:14:19 +0100 (Thu, 26 Feb 2015) | 7 lines

Changed paths:
M       cg_vbm_defaults.m
M       html/vbm12.html

Set cg_vbm_defaults.m to standard values without debugging.


------------------------------------------------------------------------
r675 | dahnke | 2015-02-26 09:58:05 +0100 (Thu, 26 Feb 2015) | 5 lines

Changed paths:
M       cg_vbm_write.m

(1)  Corrected "debug==0" error in "vbm_pre_LAS2" in "cg_vbm_write".

------------------------------------------------------------------------
r674 | dahnke | 2015-02-24 15:59:47 +0100 (Tue, 24 Feb 2015) | 51 lines

Changed paths:
 M      .
M       cg_vbm_defaults.m
A       cg_vbm_defaults_template_humanIXI555.m
M       cg_vbm_run_job.m
M       cg_vbm_write.m
A  +    html/vbm12_instruction_templates.html
 M      templates_animals
A       templates_animals/cg_vbm_defaults_template_primate130.m
A       templates_animals/cg_vbm_defaults_template_primate15.m
A       templates_animals/cg_vbm_defaults_template_primate400.m
A       templates_animals/cg_vbm_defaults_template_primate45.m
M       vbm_io_cgw2seg.m
M       vbm_io_img2nii.m
M       vbm_io_remat.m
M       vbm_set_cg_vbm_defaults.m
M       vbm_stat_marks.m
M       vbm_tst_CJV.m
M       vbm_tst_qa.m
M       vbm_vol_approx.m
M       vbm_vol_correct_slice_scaling.m

Major changes:
(1)  Corrected "median"-problem in "vbm_pre_gintnorm" in "cg_vbm_write".
     The median was used to estimate tissue peaks, but lightly different mask
     in different OS leaded to different tissue peaks that lead to stronger
     differences between Linux and Windows/Mac. Used rounding operations (10^-5)
     to guaranty similar values.
(2)  Corrected error in CSF/BG estimation in "vbm_pre_LAS2" in "cg_vbm_write"
     that emphasize background noise.
     Added code to improve the cortical GM segmentation, especially after the
     bias correction (LAS-WM threshold).
(3)  Changed handling of the MRF filter after spm-preprocessing2 in
     "cg_vbm_write".
(4)  Large update for "vbm_vol_correct_slice_scaling".
     Added automatic detection of slice and iteration criteria and validate the
     function for simulated artifacts in the brain web phantom. Added the private
     script "vbm_tst_BWPsliceartifact" that modifies and test images.


Minor changes:
(1)  Added help and small corrections in "cg_io_cgw2seg" and "vbm_io_img2nii.
(2)  Updated "vbm_io_remat" and added help.
(3)  Updated species specific processing in "vbm_tst_qa".
(4)  Added new "cg_vbm_defaults" for primates brain volume based primate
     templates and html-help file.
(5)  Added code to compare the preprocessing steps on different operating
     systems in "cg_vbm_run_job" and "cg_vbm_run_job".
(*)  Further small corrections.


------------------------------------------------------------------------
r673 | gaser | 2015-01-27 11:46:31 +0100 (Tue, 27 Jan 2015) | 20 lines

Changed paths:
M       compile.m
M       vbm_surf_createCS.m
M       vbm_vol_eidist.c
M       vbm_vol_genus0.c

(1) Updated compile.m.
(2) Added algorithm.h in the header of vbm_vol_eidist.c.
(3) Correction for 'n' prefix in vbm_surf_createCS.m was not working for
    img-files.
(4) Added a bunch of new functions to CAT_Topology.c:
      - get_cluster_size
      - changed_voxels_between_surfaces
      - surface_deform
(5) Made a lot of changed fix_topology_sph in CAT_Topology.c:
      - estimate SPHs of surface with either handles or holes
      - estimate change in voxel space for handle/hole approach
      - choose operation with smaller change in voxel space


------------------------------------------------------------------------
r672 | gaser | 2015-01-05 09:24:34 +0100 (Mon, 05 Jan 2015) | 15 lines

Changed paths:
M       cg_vbm_run.m
M       cg_vbm_run_job.m
M       cg_vbm_write.m
M       html/vbm12.html
!       vbm_surf_createCS.m
M       vbm_tst_qa.m
!       vbm_vol_approx.m

(1) Replaced nanmean by vbm_stat_nanmean in vbm_tst_qa.m
(2) Corrected typo in cg_vbm_write.m for calculating Yqw.
(3) Added eps to division in cg_vbm_run_job.m and cg_vbm_run.



------------------------------------------------------------------------
r671 | gaser | 2014-12-16 15:46:26 +0100 (Tue, 16 Dec 2014) | 11 lines

Changed paths:
M       cg_check_cov.m
M       cg_vbm_tools.m
M       cg_vbm_write.m
M       tbx_cfg_vbm.m

(1) If no images are saved within cg_vbm_write.m the flag do_cls is set to 1
    because segmentations are necessary for ROI output and quality measures.
(2) Solved some issues in cg_vbm_tools for covariance check for surfaces.


------------------------------------------------------------------------
r670 | gaser | 2014-12-15 14:40:08 +0100 (Mon, 15 Dec 2014) | 7 lines

Changed paths:
M       cg_vbm_batch.m
M       html/vbm12.html

Solved issue with not used externel default file in cg_vbm_batch.m.


------------------------------------------------------------------------
r669 | gaser | 2014-12-12 13:26:16 +0100 (Fri, 12 Dec 2014) | 8 lines

Changed paths:
M       cg_check_cov.m
M       cg_vbm_tools.m
M       html/vbm12.html

Updated some plot functions in cg_check_cov.m for nicer output.


------------------------------------------------------------------------
r668 | gaser | 2014-12-12 10:42:11 +0100 (Fri, 12 Dec 2014) | 8 lines

Changed paths:
M       cg_check_cov.m
M       cg_vbm_tools.m
M       html/vbm12.html

Use simpler options in cg_check_cov.m.


------------------------------------------------------------------------
r667 | gaser | 2014-12-12 10:20:02 +0100 (Fri, 12 Dec 2014) | 11 lines

Changed paths:
M       cg_check_cov.m
MM      cg_vbm_longitudinal_batch.m
MM      cg_vbm_longitudinal_batch.sh
M       cg_vbm_tools.m
M       html/vbm12.html

Removed sample coding from cg_chek_cov.m and added option to sepcify different samples.



------------------------------------------------------------------------
r666 | gaser | 2014-12-11 15:53:38 +0100 (Thu, 11 Dec 2014) | 24 lines

Changed paths:
M       cg_check_cov.m
M       cg_showslice_all.m
M       cg_vbm_defaults.m
M       cg_vbm_longitudinal_batch.m
M       cg_vbm_longitudinal_batch.sh
M       cg_vbm_longitudinal_multi.m
M       cg_vbm_tools.m
M       html/vbm12.html
M       tbx_cfg_vbm.m
M       vbm_io_writenii.m
M       vbm_io_xml.m
M       vbm_plot_boxplot.m
M       vbm_surf_createCS.m

(1) Set debug to zero and solved issues with debug flag in vbm_surf_createCS.m.
(2) Corrected some typos in vbm_plot_boxplot.m and vbm_io_xml.m.
(3) vbm_io_writenii still had dartel options and extensions for writing data.
(4) Added many options to ch_check_cov to deal with different samples and
    to display quality measures in xml-files.
(5) Solved issue with 'GetWin' in cg_showslice_all.m.



------------------------------------------------------------------------
r665 | dahnke | 2014-12-10 13:51:45 +0100 (Wed, 10 Dec 2014) | 24 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_run_job.m
M       cg_vbm_write.m
M       templates_animals/ape_greater_cg_vbm_defaults.m
M       templates_animals/ape_lesser_cg_vbm_defaults.m
M       templates_animals/monkey_newworld_cg_vbm_defaults.m
M       templates_animals/monkey_oldworld_cg_vbm_defaults.m
M       vbm_io_writenii.m
M       vbm_plot_boxplot.m
M       vbm_qa_calcSTC.m
M       vbm_stat_marks.m
M       vbm_surf_createCS.m
D       vbm_tst_pre.m
M       vbm_tst_qa.m

(1)  Corrected affine registration error.
(2)  Changed vbm.opts.samp to 2 mm.
(3)  Corrected small errors.
(4)  Updated primate vbm_defaults.
(5)  Removed prefix variable in  vbm_io_writenii.
(6)  Update QA parameter.


------------------------------------------------------------------------
r664 | gaser | 2014-12-04 11:45:31 +0100 (Thu, 04 Dec 2014) | 9 lines

Changed paths:
M       Makefile.vbm
A       cg_vbm_longitudinal_batch.m
A       cg_vbm_longitudinal_batch.sh
M       cg_vbm_longitudinal_multi_run.m

Added commandline batch for longitudinal pipeline.


------------------------------------------------------------------------
r663 | gaser | 2014-12-04 10:15:06 +0100 (Thu, 04 Dec 2014) | 10 lines

Changed paths:
M       cg_vbm_longitudinal.m
M       cg_vbm_longitudinal_multi.m
M       cg_vbm_longitudinal_multi_run.m
M       cg_vbm_tools.m
 M      html/vbm12_starting.html

Updated use of modulation option for longitudinal pipeline.


------------------------------------------------------------------------
r662 | gaser | 2014-12-03 13:05:42 +0100 (Wed, 03 Dec 2014) | 16 lines

Changed paths:
M       cg_vbm_defs.m
M       cg_vbm_longitudinal.m
M       cg_vbm_tools.m
M       html/vbm12.html
M       tbx_cfg_vbm.m
M       vbm_vol_partvol.m

(1) Added modulation option for non-linear only to cg_vbm_defs.m.
(2) Replaced spm_def2det in cg_vbm_defs.m by spm_diffeo.
(3) Always use "No" instead of "None" in tbx_cfg_vbm
(4) Corrected captials and some output in vbm_vol_partitions.m.
(5) Always write modulated data non-linear-only in cg_vbm_longitudinal.m.



------------------------------------------------------------------------
r661 | gaser | 2014-12-03 10:51:22 +0100 (Wed, 03 Dec 2014) | 17 lines

Changed paths:
M       cg_vbm_tools.m
M       html/vbm12.html
M       html/vbm12_ackknowledgement.html
M       html/vbm12_instruction.html
M       html/vbm12_instruction_PP.html
M       html/vbm12_introduction.html
M       html/vbm12_methods_SBM.html
A       html/vbm12_starting.html
M       html/vbm12_stuff.html
M       vbm12.fig
M       vbm12.m

(1) Updated GUI and added some more functionality.
(2) Updated html-documentation and added quick starting guide.


------------------------------------------------------------------------
r660 | dahnke | 2014-11-25 21:08:52 +0100 (Tue, 25 Nov 2014) | 10 lines

Changed paths:
M       cg_vbm_run_job.m
M       html/vbm12_instruction_PP.html
 M      templates_1.50mm
M       vbm_plot_boxplot.m
!       vbm_tst_pre.m
D       vbm_tst_reduceRes.m

(1)  Corrected affine registration error.

------------------------------------------------------------------------
r659 | gaser | 2014-11-25 15:26:48 +0100 (Tue, 25 Nov 2014) | 7 lines

Changed paths:
M       cg_vbm_write.m
M       html/vbm12.html

Replaced additional opt.print flag in cg_vbm_write.m by general vbm.print.


------------------------------------------------------------------------
r658 | gaser | 2014-11-25 11:46:05 +0100 (Tue, 25 Nov 2014) | 7 lines

Changed paths:
M       html/vbm12.html
M       vbm12.m

Solved issue with missing function for longitduinal data in vbm12.m.


------------------------------------------------------------------------
r657 | gaser | 2014-11-25 11:13:53 +0100 (Tue, 25 Nov 2014) | 12 lines

Changed paths:
M       cg_check_cov.m
M       cg_slice_overlay.m
M       cg_slice_overlay_ui.m
M       html/vbm12.html
M       vbm12.fig
M       vbm12.m

(1) Added TFCE button that is enabled if toolbox is installed.
(2) Added flag "func" to cg_slice_overlay.m.


------------------------------------------------------------------------
r656 | gaser | 2014-11-21 16:21:34 +0100 (Fri, 21 Nov 2014) | 6 lines

Changed paths:
M       cg_vbm_write.m

In cg_vbm_write ROI option was still linked to flag extopts.


------------------------------------------------------------------------
r655 | gaser | 2014-11-21 16:06:46 +0100 (Fri, 21 Nov 2014) | 10 lines

Changed paths:
MM      cg_vbm_extopts.m
MM      cg_vbm_opts.m
M       cg_vbm_write.m
 M      vbm_vol_groupwise_ls.m
 M      vbm_vol_series_align.m

In cg_vbm_write surface option was still linked to flag extopts.


------------------------------------------------------------------------
r654 | gaser | 2014-11-21 14:53:42 +0100 (Fri, 21 Nov 2014) | 6 lines

Changed paths:
M       cg_vbm_run.m

Non-existing option dartelwarp was still used in cg_vbm_run.m.


------------------------------------------------------------------------
r653 | gaser | 2014-11-21 14:13:47 +0100 (Fri, 21 Nov 2014) | 44 lines

Changed paths:
M       Makefile.vbm
M       cg_spm_batch.sh
M       cg_vbm_batch.m
M       cg_vbm_batch.sh
M       cg_vbm_defaults.m
M       cg_vbm_defs.m
A       cg_vbm_extopts.m
M       cg_vbm_longitudinal.m
M       cg_vbm_longitudinal_multi.m
M       cg_vbm_longitudinal_multi_run.m
A       cg_vbm_opts.m
M       cg_vbm_run.m
M       cg_vbm_tools.m
M       cg_vbm_write.m
M       distribute_to_server.sh
M       html/vbm12.html
M       html/vbm12_instruction_FN.html
M       html/vbm12_instruction_PP.html
M       human_IXI555_cg_vbm_defaults.m
M       tbx_cfg_vbm.m
 M      templates_animals/monkey_oldworld_atlas_inia19NeuroMaps.csv
 M      templates_animals/monkey_oldworld_atlas_inia19NeuroMaps.txt
M       vbm12.fig
M       vbm12.m
M       vbm_io_xml.m
A       vbm_vol_groupwise_ls.m
A       vbm_vol_series_align.m

(1) Added new longitudinal pipeline that strongly relies on the serial
    longitudinal registration of the Longitudinal Toolbox in SPM12.
(2) Removed old stuff for longitduinal registration nincluding bias-
    correction between scans.
(3) Solved issue with repmat in vbm_vol_correct_slices.m.
(4) If no jvm is available vbm_io_xml.m now immediately returns.
(5) Cleaned cg_vbm_defs.m from some unused functions.

(6) Divided tbx_cfg_vbm.m in different parts for opts and extopts that can
    be now easily used by other batches (e,g, cg_vbm_longitudinal_multi.m).
(7) Removed all dartelwarp option because Dartel is now always used.
(8) Warped files are now without additional "r".
(9) Some editing in htlm files to consider new changes.


------------------------------------------------------------------------
r652 | dahnke | 2014-11-20 17:09:10 +0100 (Thu, 20 Nov 2014) | 10 lines

Changed paths:
M       cg_vbm_write.m
M       vbm_tst_calc_kappa.m
M       vbm_vol_average.m
M       vbm_vol_correct_slice_scaling.m

(1)  Simplified VBM12 report.
(2)  Corrected error in vbm_vol_correct_slice_scaling, added parameters and
     help text.

------------------------------------------------------------------------
r651 | gaser | 2014-11-19 11:13:49 +0100 (Wed, 19 Nov 2014) | 12 lines

Changed paths:
 M      fsaverage/lh.inflated.gii
 M      fsaverage/rh.inflated.gii
M       html/vbm12_methods_VBM.html
M       tbx_cfg_vbm.m
M       vbm_surf_resamp.m

(1) Solved resampling issue. The underlying resampled surface is now always
    the non-linearely registered surface.
(2) Some editing in html/vbm12_methods_VBM.html.


------------------------------------------------------------------------
r650 | dahnke | 2014-11-18 17:15:36 +0100 (Tue, 18 Nov 2014) | 33 lines

Changed paths:
 M      .
M       cg_vbm_defaults.m
M       cg_vbm_run.m
M       cg_vbm_run_job.m
M       cg_vbm_write.m
 M      html
M       html/vbm12_instruction_PP.html
 M      html/vbm_vol_correct_slice_scaling_768.png
A       human_IXI555_cg_vbm_defaults.m
M       tbx_cfg_vbm.m
 M      templates_1.50mm
 M      templates_1.50mm/brainmask.nii
 M      templates_animals
M       templates_animals/ape_greater_cg_vbm_defaults.m
M       templates_animals/ape_lesser_cg_vbm_defaults.m
M       templates_animals/monkey_newworld_cg_vbm_defaults.m
A       templates_animals/monkey_oldworld_atlas_inia19NeuroMaps.csv
A       templates_animals/monkey_oldworld_atlas_inia19NeuroMaps.nii
A       templates_animals/monkey_oldworld_atlas_inia19NeuroMaps.txt
M       templates_animals/monkey_oldworld_brainmask.nii
M       templates_animals/monkey_oldworld_cg_vbm_defaults.m
A       vbm_set_cg_vbm_defaults.m
M       vbm_surf_parameters.m
MM      vbm_vol_correct_slice_scaling.m

(1)  Added "vbm_set_cg_vbm_defaults" to change the cg_vbm_defaults file e.g.
     for non-human data.
(2)  Corrected error in animal-defaults-files.
(3)  Corrected vbm12 atlas setting errors.



------------------------------------------------------------------------
r649 | dahnke | 2014-11-14 12:53:44 +0100 (Fri, 14 Nov 2014) | 103 lines

Changed paths:
 M      .
D       brainmask_LPBA40.nii
D       brainmask_LPBA40_dartel.nii
M       cg_vbm_batch.m
M       cg_vbm_batch.sh
M       cg_vbm_defaults.m
M       cg_vbm_run.m
M       cg_vbm_run_job.m
M       cg_vbm_run_newcatch.m
M       cg_vbm_write.m
M       distribute_to_server.sh
M       html/vbm12_FAQ.html
A       html/vbm_vol_correct_slice_scaling_768.png
D       submask.nii
M       tbx_cfg_vbm.m
 M      templates_1.50mm
A       templates_1.50mm/brainmask.nii
A       templates_animals
A       templates_animals/ape_greater_T1.nii
A       templates_animals/ape_greater_T2.nii
A       templates_animals/ape_greater_TPM.nii
A       templates_animals/ape_greater_TPMt.nii
A       templates_animals/ape_greater_Template_1.nii
A       templates_animals/ape_greater_Template_2.nii
A       templates_animals/ape_greater_Template_3.nii
A       templates_animals/ape_greater_Template_4.nii
A       templates_animals/ape_greater_Template_5.nii
A       templates_animals/ape_greater_Template_6.nii
A       templates_animals/ape_greater_brainmask.nii
A       templates_animals/ape_greater_cg_vbm_defaults.m
A       templates_animals/ape_greater_vbm12.nii
A       templates_animals/ape_lesser_T1.nii
A       templates_animals/ape_lesser_T2.nii
A       templates_animals/ape_lesser_TPM.nii
A       templates_animals/ape_lesser_brainmask.nii
A       templates_animals/ape_lesser_cg_vbm_defaults.m
A       templates_animals/monkey_newworld_T1.nii
A       templates_animals/monkey_newworld_T2.nii
A       templates_animals/monkey_newworld_TPM.nii
A       templates_animals/monkey_newworld_brainmask.nii
A       templates_animals/monkey_newworld_cg_vbm_defaults.m
A       templates_animals/monkey_oldworld_T1.nii
A       templates_animals/monkey_oldworld_T2.nii
A       templates_animals/monkey_oldworld_TPM.nii
A       templates_animals/monkey_oldworld_Template_1.nii
A       templates_animals/monkey_oldworld_Template_2.nii
A       templates_animals/monkey_oldworld_Template_3.nii
A       templates_animals/monkey_oldworld_Template_4.nii
A       templates_animals/monkey_oldworld_Template_5.nii
A       templates_animals/monkey_oldworld_Template_6.nii
A       templates_animals/monkey_oldworld_brainmask.nii
A       templates_animals/monkey_oldworld_cg_vbm_defaults.m
A       templates_animals/monkey_oldworld_vbm12.nii
D       vbm_db.m
D       vbm_db_batch.m
M       vbm_io_csv.m
D       vbm_io_mysql.m
M       vbm_stat_marks.m
D       vbm_tst_SRS.m
D       vbm_tst_calc_bias.m
M       vbm_tst_pre.m
M       vbm_tst_qa.m
D       vbm_tst_qa_groups.m
D       vbm_tst_qa_groups_test.m
M       vbm_vol_atlas.m
M       vbm_vol_average.m
A       vbm_vol_correct_slice_scaling.m
M       vbm_vol_iscale.m
M       vbm_vol_partvol.m
M       vbm_vol_sanlm.m
M       vbm_vol_smooth3X.m

(1)  Removed private or unnecessary files:
     * vbm_tst_qa_groups.m           - private - NISALS QA - out of date
     * vbm_tst_qa_groups_test.m      - private - NISALS QA - out of date
     * brainmask_LPBA40_dartel.nii   - unused
     * brainmask_LPBA40.nii          - unused
     * submask.nii                   - unused / private
     * vbm_db                        - private - NISALS QA - out of date
     * vbm_db_batch                  - private - NISALS QA - out of date
     * vbm_io_mysql                  - private - NISALS QA - out of date
     * vbm_tst_SRS                   - private
     * vbm_tst_calc_bias             - private - qa script - out of date
(2)  Updated "vbm_vol_sanlm".
(3)  Added function to correct slice intensity errors
     "vbm_vol_corrected_slice_scaling" that based on "cg_correct_slice_scaling".
(4)  Prepare multi species processing:
     Added "species" variable to batch and add further default-files.
     Added 4 further primate species:
      - ape_greater:     chimpanzees, bonobos, gorillas, orang-utans
      - apes_lesser:     gibbons
      - monkey_oldworld: baboons, macaques
      - monkey_newwold:  squirrels, ...
     The maps of this species are located in the "templates_animal" directory.
     Each species comes with TPM, T1, T2, brainmask, vbm12, and Dartel
     template maps.
(5)  Corrected "Warning: Control Character '\U'" in "cg_vbm_run_newcatch 19" by
     replacing '\' by '\\'.
(6)  The "textscan" function in "vbm_io_csv" requires for MATLAB>2013 no
     "BufSize" variable and throw warnings. Added distinction by cases.
(7)  Corrected GUI variable name errors.

------------------------------------------------------------------------
r648 | gaser | 2014-11-13 10:44:24 +0100 (Thu, 13 Nov 2014) | 9 lines

Changed paths:
M       html/vbm12.html
M       vbm12.fig
M       vbm_surf_resamp.m

(1) Slightly changed GUI buttons.
(2) Resampled values without smoothing will skip the s*mm. as prepend.


------------------------------------------------------------------------
r647 | gaser | 2014-11-13 08:39:10 +0100 (Thu, 13 Nov 2014) | 8 lines

Changed paths:
A       fsaverage/lh.inflated.gii
A       fsaverage/rh.inflated.gii
M       html/vbm12.html

Added inflated surfaces to fsaverage for display purposes.


------------------------------------------------------------------------
r646 | gaser | 2014-11-11 09:23:41 +0100 (Tue, 11 Nov 2014) | 10 lines

Changed paths:
M       html/vbm12.html
M       vbm_surf_createCS.m

(1) Added CAT_RefineMesh after reduce_patch in vbm_surf_createCS.m because
    reducing patch leads to huge triangles in some areas.
(2) Flag usePPmap is again set to "0" because CAT_DeformSurface did not worked
    properly.


------------------------------------------------------------------------
r645 | gaser | 2014-11-06 14:15:28 +0100 (Thu, 06 Nov 2014) | 13 lines

Changed paths:
M       cg_vbm_tools.m
M       html/vbm12.html
M       vbm_surf_createCS.m
M       vbm_surf_parameters.m

(1) Added areal smoothing to spherical inflation to obtain more equally
    sized spheres.
(2) Removed estimation of local surface area because it worked not yet
    correctly.



------------------------------------------------------------------------
r644 | gaser | 2014-11-05 12:09:30 +0100 (Wed, 05 Nov 2014) | 11 lines

Changed paths:
M       cg_spmF2x.m
M       cg_spmT2x.m
M       cg_vbm_tools.m
M       vbm_surf_parameters.m

(1) Added estimation of sucus depth and surface area and updated all
    relevant functions.
(2) Corrected bug in spmT2x.m and spmF2x regarding wrong filenames.


------------------------------------------------------------------------
r643 | dahnke | 2014-10-24 17:50:36 +0200 (Fri, 24 Oct 2014) | 19 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_write.m
A       templates_1.50mm/aal.xml
A       templates_1.50mm/hammers.xml
A       templates_1.50mm/ibsr.xml
A       templates_1.50mm/mori.xml
A       templates_1.50mm/neuromorphometrics.csv
A       templates_1.50mm/neuromorphometrics.nii
A       templates_1.50mm/neuromorphometrics.txt
A       templates_1.50mm/neuromorphometrics.xml
M       vbm_stat_marks.m
M       vbm_vol_atlas.m

(1)  Moved code block "deformation output" in cg_vbm_write to "write output" section.
(2)  Update command line report.
(3)  Added atlas-xml files for SPM12-ROI analysis (alpha version).
(4)  Added neuromorphometrics atlas (alpha version).

------------------------------------------------------------------------
r642 | gaser | 2014-10-24 10:14:11 +0200 (Fri, 24 Oct 2014) | 7 lines

Changed paths:
M       cg_vbm_batch.m
M       html/vbm12.html

Adapted cg_vbm_batch.m to new parameters.


------------------------------------------------------------------------
r641 | gaser | 2014-10-23 16:10:57 +0200 (Thu, 23 Oct 2014) | 6 lines

Changed paths:
M       cg_vbm_write.m
M       html/vbm12.html

Yb was too early deleted for further surface use.

------------------------------------------------------------------------
r640 | dahnke | 2014-10-23 12:11:37 +0200 (Thu, 23 Oct 2014) | 6 lines

Changed paths:
M       cg_vbm_defs.m

(1)  Added spm_load_float (that was removed in SPM12) into cg_vbm_defs (the only
     function that requires this function.

------------------------------------------------------------------------
r639 | dahnke | 2014-10-23 12:03:54 +0200 (Thu, 23 Oct 2014) | 9 lines

Changed paths:
M       cg_vbm_run_newcatch.m
M       cg_vbm_write.m
M       vbm_vol_atlas.m

(1)  Corrected report error in cg_vbm_write.
(2)  Corrected error handling in cg_vbm_run_newcatch.
(3)  Prepared further atlas data and xml export in vbm_vol_atlas (not read yet).

------------------------------------------------------------------------
r638 | gaser | 2014-10-23 11:49:46 +0200 (Thu, 23 Oct 2014) | 7 lines

Changed paths:
M       cg_vbm_defaults.m
M       html/vbm12.html

Set sanlm flag in cg_vbm_defaults again to "3".


------------------------------------------------------------------------
r637 | gaser | 2014-10-23 11:48:36 +0200 (Thu, 23 Oct 2014) | 10 lines

Changed paths:
M       cg_vbm_run_job.m
M       tbx_cfg_vbm.m
M       vbm_spm.m

(1) Added rician flag to cg_vbm_run_job.m.
(2) Added some comments in vbm_spm.m.
(3) Many edits and formattings in tbx_cfg_vbm.m.


------------------------------------------------------------------------
r636 | dahnke | 2014-10-23 08:27:41 +0200 (Thu, 23 Oct 2014) | 8 lines

Changed paths:
M       vbm12.fig
M       vbm12.m
M       vbm_tst_pre.m
M       vbm_vol_atlas.m

(1)  Added VBM12 header figure in VBM12 GUI.

------------------------------------------------------------------------
r635 | dahnke | 2014-10-22 14:18:51 +0200 (Wed, 22 Oct 2014) | 27 lines

Changed paths:
 M      .
M       cg_vbm_batch.m
M       cg_vbm_defaults.m
M       cg_vbm_run.m
M       cg_vbm_run_job.m
M       cg_vbm_write.m
M       tbx_cfg_vbm.m
M       vbm_stat_marks.m
M       vbm_tst_pre.m
M       vbm_tst_qa.m
M       vbm_vol_eidist.c

(1)  Corrected to strong CSF/GM cleanup (cg_vbm_write - cleanup section).
(2)  Corrected CSF threshold problem for bad SPM segmentation of the global
     intensity scaling (cg_vbm_write > vbm_pre_gintnorm).
(3)  Added "extopts.sanlm==5" backend option and code to use only the ORNLM
     filter to avoid problems with untypical noise (cg_vbm_write - noise
     correction section)
(4)  Corrected CSF/GM map creation for bad SPM segmentations and local CSF/back-
     ground estimation (cg_vbm_write > vbm_pre_LAS).
(5)  Added "extopts.NCstr==0.5" paramter to control the strength of the ORNLM
     and MRF noise correction.
(6)  Corrected interpolation behavior to guaranty Dartel resolution in any case.
(7)  Updated VBM12 report.


------------------------------------------------------------------------
r634 | gaser | 2014-10-22 12:09:12 +0200 (Wed, 22 Oct 2014) | 7 lines

Changed paths:
M       cg_vbm_tools.m
M       html/vbm12.html

Did some formatting in cg_vbm_tools.m.


------------------------------------------------------------------------
r633 | gaser | 2014-10-22 11:11:50 +0200 (Wed, 22 Oct 2014) | 9 lines

Changed paths:
M       cg_vbm_tools.m
M       html/vbm12.html
M       html/vbm12.txt
M       html/vbm12_instruction_FF.html

Corrected typo in cg_vbm_tools.


------------------------------------------------------------------------
r632 | gaser | 2014-10-22 11:06:47 +0200 (Wed, 22 Oct 2014) | 10 lines

Changed paths:

(1) Added rician option to sanlm_float.c and sanlMex.c to allow to disable
    Rician noise estimation that causes artefacts in the neighbourhood
    of high signal intensities.
(2) Modified vbm_vol_sanlm.m and cg_vbm_tools.m to consider rician option.
(3) Recompiled all c-files.
(4) Modified html text.


------------------------------------------------------------------------
r631 | gaser | 2014-10-22 11:05:46 +0200 (Wed, 22 Oct 2014) | 70 lines

Changed paths:
M       AmapMex.mexw32
M       AmapMex.mexw64
M       Makefile.vbm
D       cg_sanlm.m
M       cg_vbm_defaults.m
M       cg_vbm_run_job.m
M       cg_vbm_tools.m
M       cg_vbm_write.m
M       html/vbm12.html
M       html/vbm12_FAQ.html
M       html/vbm12_ackknowledgement.html
M       html/vbm12_instruction.html
M       html/vbm12_instruction_FF.html
M       html/vbm12_instruction_PP.html
M       html/vbm12_introduction.html
M       html/vbm12_methods_SBM.html
M       html/vbm12_methods_VBM.html
M       html/vbm12_stuff.html
M       ornlmMex.mexw32
M       ornlmMex.mexw64
M       sanlmMex.c
M       sanlmMex.mexa64
M       sanlmMex.mexglx
M       sanlmMex.mexmaci64
M       sanlmMex.mexw32
M       sanlmMex.mexw64
M       sanlmMex_noopenmp.mexa64
M       sanlmMex_noopenmp.mexglx
M       sanlmMex_noopenmp.mexmaci64
M       sanlmMex_noopenmp.mexw32
M       sanlmMex_noopenmp.mexw64
M       sanlm_float.c
M       vbdist.mexw32
M       vbdist.mexw64
MM      vbm_tst_reduceRes.m
M       vbm_vol_downcut.mexw32
M       vbm_vol_downcut.mexw64
M       vbm_vol_eidist.mexw32
M       vbm_vol_eidist.mexw64
M       vbm_vol_genus0.mexw32
M       vbm_vol_genus0.mexw64
M       vbm_vol_gradient3.mexw32
M       vbm_vol_gradient3.mexw64
M       vbm_vol_interp3f.mexw32
M       vbm_vol_interp3f.mexw64
M       vbm_vol_laplace3.mexw32
M       vbm_vol_laplace3.mexw64
M       vbm_vol_laplace3R.mexw32
M       vbm_vol_laplace3R.mexw64
M       vbm_vol_localstat.mexw32
M       vbm_vol_localstat.mexw64
M       vbm_vol_median3.mexw32
M       vbm_vol_median3.mexw64
M       vbm_vol_median3c.mexw32
M       vbm_vol_median3c.mexw64
M       vbm_vol_pbtp.mexw32
M       vbm_vol_pbtp.mexw64
M       vbm_vol_sanlm.m
M       vbm_vol_simgrow.mexw32
M       vbm_vol_simgrow.mexw64

(1) Added rician option to sanlm_float.c and sanlMex.c to allow to disable
    Rician noise estimation that causes artefacts in the neighbourhood
    of high signal intensities.
(2) Modified vbm_vol_sanlm.m and cg_vbm_tools.m to consider rician option.
(3) Recompiled all c-files.
(4) Modified html text.


------------------------------------------------------------------------
r630 | gaser | 2014-10-20 17:19:31 +0200 (Mon, 20 Oct 2014) | 7 lines

Changed paths:

(1) Renamed txt folder to html.
(2) Changed resolution-threshold fro interpolation in cg_vbm_run_job.m.
(3) Deleted vbm12.txt


------------------------------------------------------------------------
r629 | gaser | 2014-10-20 17:18:50 +0200 (Mon, 20 Oct 2014) | 46 lines

Changed paths:
M       Makefile.vbm
M       cg_vbm_run_job.m
A  +    html
M  +    html/vbm12.html
M  +    html/vbm12.txt
M       spm_vbm12.m
D       txt
D       txt/analyse_methods.png
D       txt/contact.jpg
D       txt/cortical_measures.png
D       txt/gyrification_index.png
D       txt/home.jpg
D       txt/human_brain.en.jpg
D       txt/human_brain.png
D       txt/images.jpg
D       txt/people.jpg
D       txt/research.jpg
D       txt/rqa01-intro-bwp-real.png
D       txt/style.css
D       txt/vbm.jpg
D       txt/vbm12.html
D       txt/vbm12.txt
D       txt/vbm12_FAQ.html
D       txt/vbm12_ackknowledgement.html
D       txt/vbm12_instruction.html
D       txt/vbm12_instruction_FF.html
D       txt/vbm12_instruction_FN.html
D       txt/vbm12_instruction_MS.html
D       txt/vbm12_instruction_PP.html
D       txt/vbm12_instruction_QA.html
D       txt/vbm12_instruction_ST.html
D       txt/vbm12_introduction.html
D       txt/vbm12_methods.html
D       txt/vbm12_methods_QA.html
D       txt/vbm12_methods_RBM.html
D       txt/vbm12_methods_SBM.html
D       txt/vbm12_methods_VBM.html
D       txt/vbm12_stuff.html
D       vbm12.txt

(1) Renamed txt folder to html.
(2) Changed resolution-threshold fro interpolation in cg_vbm_run_job.m.
(3) Deleted vbm12.txt


------------------------------------------------------------------------
r628 | dahnke | 2014-10-20 16:49:28 +0200 (Mon, 20 Oct 2014) | 65 lines

Changed paths:
 M      .
M       CHANGES.txt
M       cg_vbm_batch.m
M       cg_vbm_defaults.m
M       cg_vbm_run_job.m
M       cg_vbm_run_newcatch.m
M       cg_vbm_write.m
M       spm_vbm12.m
A       txt
A       txt/analyse_methods.png
A       txt/contact.jpg
A       txt/cortical_measures.png
A       txt/gyrification_index.png
A       txt/home.jpg
A       txt/human_brain.en.jpg
A       txt/human_brain.png
A       txt/images.jpg
A       txt/people.jpg
A       txt/research.jpg
A       txt/rqa01-intro-bwp-real.png
A       txt/style.css
A       txt/vbm.jpg
A       txt/vbm12.html
A       txt/vbm12.txt
A       txt/vbm12_FAQ.html
A       txt/vbm12_ackknowledgement.html
A       txt/vbm12_instruction.html
A       txt/vbm12_instruction_FF.html
A       txt/vbm12_instruction_FN.html
A       txt/vbm12_instruction_MS.html
A       txt/vbm12_instruction_PP.html
A       txt/vbm12_instruction_QA.html
A       txt/vbm12_instruction_ST.html
A       txt/vbm12_introduction.html
A       txt/vbm12_methods.html
A       txt/vbm12_methods_QA.html
A       txt/vbm12_methods_RBM.html
A       txt/vbm12_methods_SBM.html
A       txt/vbm12_methods_VBM.html
A       txt/vbm12_stuff.html
M       vbm_findfiles.m
M       vbm_io_csv.m
M       vbm_io_writenii.m
M       vbm_io_xml.m
M       vbm_stat_marks.m
M       vbm_surf_createCS.m
M       vbm_tst_calc_kappa.m
M       vbm_tst_pre.m
M       vbm_tst_qa.m
A       vbm_tst_reduceRes.m
A       vbm_vol_imcalc.m

(1)  Changed input limitation for resolution properties in "cg_vbm_run_job".
(2)  Corrected cleanup error with to strong corrections in the cerebellum of the
     BWP and images with low resolutions in "cg_vbm_write".
(3)  Initialize new VBM12 help with subdirectory for HTML help files.
(4)  Added resampling function in "vbm_tst_calc_kappa" for unequal resolutions.
(5)  Added kappa-depending result coloration in "vbm_tst_calc_kappa".
(6)  Added intern interpolation routine in "cg_vbm_run_job" and extended
     "vbm_io_writenii" and "vbm_tst_qa" for downsampling of interpolated data
     back to native space.
(7)  Corrected CSF-background problems in global intensity scaling function
     "vbm_pre_gintnorm" in "cg_vbm_write.m".

------------------------------------------------------------------------
r627 | gaser | 2014-10-20 12:23:26 +0200 (Mon, 20 Oct 2014) | 8 lines

Changed paths:
M       cg_vbm_write.m
 M      vbm12.fig
 M      vbm12.m

In cg_vbm_write.m wi and mi were mixed up at line 1469.


------------------------------------------------------------------------
r626 | gaser | 2014-10-02 16:28:51 +0200 (Thu, 02 Oct 2014) | 7 lines

Changed paths:
M       Makefile.vbm
M       distribute_to_server.sh

Adapted paths to new SPM12 version (no beta anymore!).


------------------------------------------------------------------------
r625 | gaser | 2014-10-02 15:27:36 +0200 (Thu, 02 Oct 2014) | 10 lines

Changed paths:
M       Makefile.vbm
M       cg_vbm_defaults.m
M       spm_vbm12.m
A       vbm12.fig
A       vbm12.m

Added GUI interface.


------------------------------------------------------------------------
r624 | gaser | 2014-10-01 12:50:58 +0200 (Wed, 01 Oct 2014) | 6 lines

Changed paths:
M       spm_vbm12.m

Again updated update function and welcome message which is now coded in HTML.


------------------------------------------------------------------------
r623 | gaser | 2014-10-01 12:45:11 +0200 (Wed, 01 Oct 2014) | 8 lines

Changed paths:
M       cg_vbm_update.m
M       spm_vbm12.m
M       vbm12.txt

Again updated update function and welcome message which is now coded in HTML.


------------------------------------------------------------------------
r622 | gaser | 2014-10-01 11:36:12 +0200 (Wed, 01 Oct 2014) | 10 lines

Changed paths:
M       Makefile.vbm
M       cg_vbm_update.m
M       spm_vbm12.m
M       vbm12.man
M       vbm12.txt

Updated update function and welcome message which is now coded in HTML.


------------------------------------------------------------------------
r621 | gaser | 2014-09-30 12:16:11 +0200 (Tue, 30 Sep 2014) | 6 lines

Changed paths:
M       vbm_spm.m

SPM is saved using spm_get_defaults('mat.format') in spm_vbm.m.


------------------------------------------------------------------------
r620 | gaser | 2014-09-29 17:23:28 +0200 (Mon, 29 Sep 2014) | 7 lines

Changed paths:
M       cg_vbm_write.m
M       vbm12.man

spm_progress_bar was not cleared in cg_vbm_write.m.


------------------------------------------------------------------------
r619 | gaser | 2014-09-29 17:13:57 +0200 (Mon, 29 Sep 2014) | 7 lines

Changed paths:
M       cg_vbm_write.m
M       vbm12.man

Added denoising of initial spm segmentation using spm_mrf.


------------------------------------------------------------------------
r618 | gaser | 2014-09-29 15:06:01 +0200 (Mon, 29 Sep 2014) | 9 lines

Changed paths:
M       cg_vbm_write.m
M       vbm12.man

(1) Again corrected output of processing time in cg_vbm_write.m and
    vbm_surf_createCS.m.
(2) ornlm_str was missing if only SANLM filter was used in cg_vbm_write.m.


------------------------------------------------------------------------
r617 | gaser | 2014-09-29 14:10:58 +0200 (Mon, 29 Sep 2014) | 10 lines

Changed paths:
M       cg_vbm_write.m
M       vbm12.man
M       vbm_surf_createCS.m

(1) Again corrected output of processing time in cg_vbm_write.m and
    vbm_surf_createCS.m.
(2) ornlm_str was missing if only SANLM filter was used in cg_vbm_write.m.


------------------------------------------------------------------------
r616 | gaser | 2014-09-29 11:20:40 +0200 (Mon, 29 Sep 2014) | 17 lines

Changed paths:
M       Makefile.vbm
M       cg_vbm_write.m
M       compile.m
M       tbx_cfg_vbm.m
M       vbm12.man
M       vbm_io_cmd.m
M       vbm_surf_createCS.m

(1) Corrected output of processing time in cg_vbm_write.m and
    vbm_surf_createCS.m.
(2) Some minor modication to GUI-text.
(3) Modified compile tool.
(4) Handling of exlusively saving jacobian was not correct.



------------------------------------------------------------------------
r615 | dahnke | 2014-09-25 13:51:15 +0200 (Thu, 25 Sep 2014) | 6 lines

Changed paths:
M       cg_vbm_write.m
M       vbm_tst_pre.m

(1)  Corrected error in LAS class correction that cause problems with the WMHC.

------------------------------------------------------------------------
r614 | dahnke | 2014-09-25 01:09:15 +0200 (Thu, 25 Sep 2014) | 8 lines

Changed paths:
M       cg_vbm_write.m
M       vbm_stat_marks.m

(1)  Corrected QA execution error.



------------------------------------------------------------------------
r613 | dahnke | 2014-09-24 18:21:40 +0200 (Wed, 24 Sep 2014) | 9 lines

Changed paths:
D       avgT1_Dartel_IXI550_MNI152.nii
M       cg_vbm_write.m

(1)  Removed 3rd noise correction after LAS.
(2)  Corrected intensity normalization error in 7T data.
(3)  Removed old average T1 IXI image in VBM main directory.
     A new average T1 can be found in the "template_1.50mm" directory.

------------------------------------------------------------------------
r612 | gaser | 2014-09-24 17:17:18 +0200 (Wed, 24 Sep 2014) | 74 lines

Changed paths:
M       AmapMex.mexmaci64
M       AmapMex.mexw32
M       AmapMex.mexw64
M       CHANGES.txt
M       compile.m
M       ornlmMex.mexmaci64
M       ornlmMex.mexw32
M       ornlmMex.mexw64
M       sanlmMex.mexa64
M       sanlmMex.mexglx
M       sanlmMex.mexmaci64
M       sanlmMex.mexw32
M       sanlmMex.mexw64
M       sanlmMex_noopenmp.mexa64
M       sanlmMex_noopenmp.mexglx
M       sanlmMex_noopenmp.mexmaci64
M       sanlmMex_noopenmp.mexw32
M       sanlmMex_noopenmp.mexw64
M       sanlm_float.c
M       vbdist.mexglx
M       vbdist.mexmaci64
M       vbdist.mexw32
M       vbdist.mexw64
M       vbm_vol_downcut.mexglx
M       vbm_vol_downcut.mexmaci64
M       vbm_vol_downcut.mexw32
M       vbm_vol_downcut.mexw64
M       vbm_vol_eidist.mexglx
M       vbm_vol_eidist.mexmaci64
M       vbm_vol_eidist.mexw32
M       vbm_vol_eidist.mexw64
M       vbm_vol_genus0.mexglx
M       vbm_vol_genus0.mexmaci64
M       vbm_vol_genus0.mexw32
M       vbm_vol_genus0.mexw64
M       vbm_vol_gradient3.mexglx
M       vbm_vol_gradient3.mexmaci64
M       vbm_vol_gradient3.mexw32
M       vbm_vol_gradient3.mexw64
M       vbm_vol_interp3f.mexmaci64
M       vbm_vol_interp3f.mexw32
M       vbm_vol_interp3f.mexw64
M       vbm_vol_laplace3.mexglx
M       vbm_vol_laplace3.mexmaci64
M       vbm_vol_laplace3.mexw32
M       vbm_vol_laplace3.mexw64
M       vbm_vol_laplace3R.mexglx
M       vbm_vol_laplace3R.mexmaci64
M       vbm_vol_laplace3R.mexw32
M       vbm_vol_laplace3R.mexw64
M       vbm_vol_localstat.mexglx
M       vbm_vol_localstat.mexmaci64
M       vbm_vol_localstat.mexw32
M       vbm_vol_localstat.mexw64
M       vbm_vol_median3.mexglx
M       vbm_vol_median3.mexmaci64
M       vbm_vol_median3.mexw32
M       vbm_vol_median3.mexw64
M       vbm_vol_median3c.mexmaci64
M       vbm_vol_median3c.mexw32
M       vbm_vol_median3c.mexw64
M       vbm_vol_pbtp.mexmaci64
M       vbm_vol_pbtp.mexw32
M       vbm_vol_pbtp.mexw64
M       vbm_vol_simgrow.mexglx
M       vbm_vol_simgrow.mexmaci64
M       vbm_vol_simgrow.mexw32
M       vbm_vol_simgrow.mexw64

(1) SANLM-Filter had issues in white matter because of error in NAN.
(2) Recompiled all mex-files.


------------------------------------------------------------------------
r611 | dahnke | 2014-09-24 16:34:01 +0200 (Wed, 24 Sep 2014) | 18 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_write.m
A  +    templates_1.50mm/Template_T1_IXI555_MNI152.nii
D       templates_1.50mm/Template_vbm12R593a_IXI556_MNI152_T1.nii
M       vbm_plot_boxplot.m
M       vbm_stat_marks.m
M       vbm_tst_SRS.m
M       vbm_tst_calc_kappa.m
M       vbm_tst_qa.m
M       vbm_vol_atlas.m

(1)  Updated VBM report.
(2)  Added comments in "vbm_cg_defaults".
(3)  Corrected output of "vbm_tst_calc_kappa".
(4)  Updated QA functions and ratings.


------------------------------------------------------------------------
r610 | gaser | 2014-09-24 10:18:03 +0200 (Wed, 24 Sep 2014) | 8 lines

Changed paths:
M       Makefile.vbm
M       spm_vbm12.m
MM      vbm_surf_resamp_freesurfer.m

Modified CAT_FixTopology.c in CAT to consider issues with large defects.


------------------------------------------------------------------------
r609 | gaser | 2014-09-23 16:43:01 +0200 (Tue, 23 Sep 2014) | 7 lines

Changed paths:
M       cg_vbm_write.m
M       vbm12.man

Removed error in cg_vbm_write.m for undefined method 'colon'.


------------------------------------------------------------------------
r608 | gaser | 2014-09-22 13:45:20 +0200 (Mon, 22 Sep 2014) | 6 lines

Changed paths:
A       vbm_surf_resamp_freesurfer.m

Added vbm_surf_resamp_freesurfer.m to resample freesurfer data to gifti.


------------------------------------------------------------------------
r607 | gaser | 2014-09-22 13:29:37 +0200 (Mon, 22 Sep 2014) | 6 lines

Changed paths:
M       cg_vbm_write.m

Dartel was wrongly deselected if surfaces awere written, but no normalized
images.

------------------------------------------------------------------------
r606 | gaser | 2014-09-22 13:17:26 +0200 (Mon, 22 Sep 2014) | 6 lines

Changed paths:
M       vbm_surf_createCS.m

Force saving compressed gifti because ASCII format caused trouble with CAT.


------------------------------------------------------------------------
r605 | gaser | 2014-09-19 15:53:49 +0200 (Fri, 19 Sep 2014) | 10 lines

Changed paths:
M       cg_vbm_batch.m
 M      fsaverage/lh.sphere.gii
 M      fsaverage/rh.sphere.gii
M       vbm12.man
M       vbm_surf_createCS.m

Manual flipping of vertices according to vmat in vbm_surf_createCS.m did
not considered all potential cases.

------------------------------------------------------------------------
r604 | gaser | 2014-09-19 11:48:16 +0200 (Fri, 19 Sep 2014) | 7 lines

Changed paths:
M       cg_vbm_write.m
M       vbm12.man
M       vbm_surf_createCS.m

some small bugs removed...

------------------------------------------------------------------------
r603 | gaser | 2014-09-19 10:31:06 +0200 (Fri, 19 Sep 2014) | 99 lines

Changed paths:
M       AmapMex.mexw32
M       AmapMex.mexw64
M       MrfPrior.c
M       Pve.c
M       cg_vbm_defaults.m
M       cg_vbm_run.m
M       cg_vbm_tools.m
M       cg_vbm_write.m
M       compile.m
 M      compile_test_debug.m
D       fsaverage/lh.central
D       fsaverage/lh.sphere
A       fsaverage/lh.sphere.gii
D       fsaverage/rh.central
D       fsaverage/rh.sphere
A       fsaverage/rh.sphere.gii
M       ornlmMex.mexw32
M       ornlmMex.mexw64
M       sanlmMex.mexa64
M       sanlmMex.mexmaci64
M       sanlmMex.mexw32
M       sanlmMex.mexw64
M       sanlmMex_noopenmp.mexa64
M       sanlmMex_noopenmp.mexglx
M       sanlmMex_noopenmp.mexmaci64
M       sanlmMex_noopenmp.mexw32
M       sanlmMex_noopenmp.mexw64
M       sanlm_float.c
M       spm_vbm12.m
M       tbx_cfg_vbm.m
M       vbdist.c
M       vbdist.mexa64
M       vbdist.mexmaci64
M       vbdist.mexw32
M       vbdist.mexw64
M       vbm12.man
M       vbm_surf_createCS.m
M       vbm_surf_parameters.m
M       vbm_surf_resamp.m
M       vbm_vol_downcut.c
M       vbm_vol_downcut.mexw32
M       vbm_vol_downcut.mexw64
M       vbm_vol_eidist.c
M       vbm_vol_eidist.mexa64
M       vbm_vol_eidist.mexw32
M       vbm_vol_eidist.mexw64
M       vbm_vol_genus0.c
M       vbm_vol_genus0.mexa64
M       vbm_vol_genus0.mexmaci64
M       vbm_vol_genus0.mexw32
M       vbm_vol_genus0.mexw64
M       vbm_vol_gradient3.c
M       vbm_vol_gradient3.mexa64
M       vbm_vol_gradient3.mexmaci64
M       vbm_vol_gradient3.mexw32
M       vbm_vol_gradient3.mexw64
M       vbm_vol_interp3f.mexw32
M       vbm_vol_interp3f.mexw64
M       vbm_vol_laplace3.c
M       vbm_vol_laplace3.mexa64
M       vbm_vol_laplace3.mexmaci64
M       vbm_vol_laplace3.mexw32
M       vbm_vol_laplace3.mexw64
M       vbm_vol_laplace3R.c
M       vbm_vol_laplace3R.mexa64
M       vbm_vol_laplace3R.mexmaci64
M       vbm_vol_laplace3R.mexw32
M       vbm_vol_laplace3R.mexw64
M       vbm_vol_localstat.c
M       vbm_vol_localstat.mexa64
M       vbm_vol_localstat.mexmaci64
M       vbm_vol_localstat.mexw32
M       vbm_vol_localstat.mexw64
M       vbm_vol_median3.c
M       vbm_vol_median3.mexa64
M       vbm_vol_median3.mexmaci64
M       vbm_vol_median3.mexw32
M       vbm_vol_median3.mexw64
M       vbm_vol_median3c.mexw32
M       vbm_vol_median3c.mexw64
M       vbm_vol_pbtp.mexw32
M       vbm_vol_pbtp.mexw64
M       vbm_vol_simgrow.c
M       vbm_vol_simgrow.mexa64
M       vbm_vol_simgrow.mexw32
M       vbm_vol_simgrow.mexw64

(1) CAT is now using gifti formaz as default because fucking windows
    was not accepting freesurfer files.
(2) Updated surface filenames to gifti.
(3) Removed parameters bb and vox from GUI.
(4) No distiction at GUI level whether estimate or write segmentations.
(5) Handling of sanlm/ornlm flags was still not yet correct.
(6) Added strict testing in compile script.
(7) Cleaned some code according to new warnings from #6.
(8) Recompiled all CAT- and mex-files.


------------------------------------------------------------------------
r602 | dahnke | 2014-09-16 16:12:44 +0200 (Tue, 16 Sep 2014) | 23 lines

Changed paths:
M       cg_vbm_batch.m
M       cg_vbm_defaults.m
M       cg_vbm_run.m
M       cg_vbm_write.m
A       templates_1.50mm/Template_vbm12R593a_IXI556_MNI152_T1.nii
M       vbm_io_xml.m
M       vbm_stat_marks.m
M       vbm_tst_qa.m
M       vbm_vol_atlas.m
M       vbm_vol_partvol.m

(1)  Updated atlas variables and set Hammers atlas as default atlas.
(2)  Corrected MATLAB 7.4 try-catch-error in "vbm_io_xml".
(3)  Added new T1 average image "Template_vbm12R593a_IXI556_MNI152_T1.nii"
     in "templates_1.50mm" directory.
(4)  Modified bias marking. Worst case is now 200% BWP inhomogeneity that
     is around 2 times of the minimum tissue contrast.
(5)  Removed AMAP "kmeans" and "bias_fwhm" options in "cg_vbm_defaults".
(6)  Removed "LAS", "gcut", and "cleanup" options in "cg_vbm_defaults".
(7)  Updated "LASstr", "gcutstr", "cleanupstr" options in "cg_vbm_defaults".


------------------------------------------------------------------------
r601 | gaser | 2014-09-15 08:24:54 +0200 (Mon, 15 Sep 2014) | 54 lines

Changed paths:
M       AmapMex.mexw32
M       AmapMex.mexw64
M       cg_vbm_batch.m
M       cg_vbm_batch.sh
M       compile.m
A       compile_test_debug.m
M       ornlmMex.mexw32
M       ornlmMex.mexw64
M       sanlmMex.mexa64
M       sanlmMex.mexw32
M       sanlmMex.mexw64
M       sanlmMex_noopenmp.mexw32
M       sanlmMex_noopenmp.mexw64
M       tbx_cfg_vbm.m
M       vbdist.mexw32
M       vbdist.mexw64
M       vbm_vol_downcut.mexw32
M       vbm_vol_downcut.mexw64
M       vbm_vol_eidist.mexw32
M       vbm_vol_eidist.mexw64
M       vbm_vol_eikonal3.mexw64
M       vbm_vol_genus0.mexw32
M       vbm_vol_genus0.mexw64
M       vbm_vol_gradient3.mexw32
M       vbm_vol_gradient3.mexw64
M       vbm_vol_interp3f.mexw32
M       vbm_vol_interp3f.mexw64
M       vbm_vol_laplace3.mexw32
M       vbm_vol_laplace3.mexw64
M       vbm_vol_laplace3R.mexw32
M       vbm_vol_laplace3R.mexw64
M       vbm_vol_localstat.c
M       vbm_vol_localstat.mexa64
M       vbm_vol_localstat.mexglx
M       vbm_vol_localstat.mexmaci64
M       vbm_vol_localstat.mexw32
M       vbm_vol_localstat.mexw64
M       vbm_vol_median3.mexw32
M       vbm_vol_median3.mexw64
M       vbm_vol_median3c.mexw32
M       vbm_vol_median3c.mexw64
M       vbm_vol_pbtp.mexw32
M       vbm_vol_pbtp.mexw64
M       vbm_vol_simgrow.mexw32
M       vbm_vol_simgrow.mexw64

(1) Updated compile-tool and added test tool where save results after
    compilation can be compared: compile_test_debug.m.
(2) Replaced roundf from vbm_vol_localstats with ROUND macro.
(3) Some tags in tbx_cfg_vbm were not correct and mixed.
(4) Default folder for log-file in cg_vbm_bash is now PWD.


------------------------------------------------------------------------
r600 | gaser | 2014-09-12 13:13:55 +0200 (Fri, 12 Sep 2014) | 18 lines

Changed paths:
D       cg_boxplot.m
M       cg_check_cov.m
M       cg_vbm_defaults.m
M       cg_vbm_run.m
M       cg_vbm_run_job.m
M       cg_vbm_tools.m
M       cg_vbm_write.m
M       tbx_cfg_vbm.m
M       vbm_tst_qa.m
M       vbm_vol_atlas.m

(1) Removed cg_boxplot.m and all calss to it because now vbm_plot_boxplot.m
    is used.
(2) Removed ngaus, samp and Dartel option as parameters from GUI.
(3) Removed modulation where it's not really necessary.


------------------------------------------------------------------------
r599 | gaser | 2014-09-11 15:36:38 +0200 (Thu, 11 Sep 2014) | 16 lines

Changed paths:
M       cg_vbm_run.m
M       cg_vbm_run_job.m
!       cg_vbm_run_newcatch.m
!       cg_vbm_run_oldcatch.m
M       cg_vbm_write.m
M       vbm12.man
M       vbm_surf_createCS.m

(1) Removed not needed flag opt.surface in vbm_surf_createCS.m
(2) Replaced windows check in vbm_surf_createCS.m by ispc.
(3) Replaced nanmean by vbm_stat_nanmean in cg_vbm_write.m.
(4) Deselection of multithreading for windows in cg_vbm_run_job.m was not
    correct and ignored ornlm filter.
(5) Forced gray colormap at the final end in cg_vbm_run.m.

------------------------------------------------------------------------
r598 | dahnke | 2014-09-10 17:01:16 +0200 (Wed, 10 Sep 2014) | 14 lines

Changed paths:
M       cg_vbm_write.m
M       distribute_to_server.sh
M       vbm_io_xml.m
M       vbm_stat_marks.m
M       vbm_tst_qa.m
M       vbm_vol_sanlm.m

(1)  Added some comments in "vbm_vol_sanlm" and "distribute_to_server.sh".
(2)  Corrected "vbm_io_xml" write error for empty structures.
(3)  Corrected small export/display errors.
(4)  Updated "vbm_tst_qa" and "vbm_stat_marks" functions for "simpler" quality
     measures that were restricted to uncorrected exor corrected images.

------------------------------------------------------------------------
r597 | gaser | 2014-09-10 13:29:00 +0200 (Wed, 10 Sep 2014) | 6 lines

Changed paths:
M       vbm_surf_createCS.m

Deselected use of CAT_DeformSurf due to non-solved issues.


------------------------------------------------------------------------
r596 | gaser | 2014-09-09 12:37:44 +0200 (Tue, 09 Sep 2014) | 9 lines

Changed paths:
M       Makefile.vbm
M       cg_vbm_write.m
M       vbm12.man
M       vbm_surf_createCS.m

(1) Use always .nii as extension in vbm_surf_createCS.m
(2) Parameter hho was only definedfor prinintg ps-file.

------------------------------------------------------------------------
r595 | dahnke | 2014-09-03 08:40:06 +0200 (Wed, 03 Sep 2014) | 40 lines

Changed paths:
 M      .
M       CHANGES.txt
M       cg_vbm_batch.m
M       cg_vbm_defaults.m
M       cg_vbm_write.m
MM      ornlm_float.c
M       tbx_cfg_vbm.m
 M      templates_1.50mm
D       templates_1.50mm/Template_0_IXI555_MNI152.nii
D       templates_1.50mm/Template_1_IXI550_MNI152.nii
M       templates_1.50mm/Template_1_IXI555_MNI152.nii
D       templates_1.50mm/Template_2_IXI550_MNI152.nii
M       templates_1.50mm/Template_2_IXI555_MNI152.nii
D       templates_1.50mm/Template_3_IXI550_MNI152.nii
M       templates_1.50mm/Template_3_IXI555_MNI152.nii
D       templates_1.50mm/Template_4_IXI550_MNI152.nii
M       templates_1.50mm/Template_4_IXI555_MNI152.nii
D       templates_1.50mm/Template_5_IXI550_MNI152.nii
M       templates_1.50mm/Template_5_IXI555_MNI152.nii
D       templates_1.50mm/Template_6_IXI550_MNI152.nii
M       templates_1.50mm/Template_6_IXI555_MNI152.nii
M       templates_1.50mm/anatomy.txt
M       templates_1.50mm/vbm12.nii
M       vbm_surf_createCS.m
M       vbm_tst_pre.m
M       vbm_vol_atlas.m
M       vbm_vol_localstat.c
M       vbm_vol_localstat.mexmaci64
M       vbm_vol_partvol.m

(1) Updated cleanup function, by adding a WM-CSF PVE correction next to the
    ventricle, the CC and the brainstem.
(2) Added cleanupstr parameter to control strength of the cleanup function.
(3) Corrected error in "vbm_vol_localstat.c".
(4) Updated IXI555 template.
(5) Removed surface defect marking for Windows systems.
(6) Prepared GUI entries for some parameter.
(7) Corrected ventricle detection in "vbm_vol_partvol".

------------------------------------------------------------------------
r594 | gaser | 2014-08-29 11:04:22 +0200 (Fri, 29 Aug 2014) | 82 lines

Changed paths:
M       AmapMex.mexmaci64
M       AmapMex.mexw32
M       AmapMex.mexw64
M       Contents_info.txt
M       Makefile.vbm
M       cg_slice_overlay.m
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       compile.m
M       ornlmMex.c
M       ornlmMex.mexa64
M       ornlmMex.mexglx
M       ornlmMex.mexmaci64
M       ornlmMex.mexw32
M       ornlmMex.mexw64
A       ornlm_float.c
M       sanlmMex.mexglx
M       sanlmMex.mexmaci64
M       sanlmMex.mexw32
M       sanlmMex.mexw64
M       sanlmMex_noopenmp.mexmaci64
M       sanlmMex_noopenmp.mexw32
M       sanlmMex_noopenmp.mexw64
M       vbdist.mexmaci64
M       vbdist.mexw32
M       vbdist.mexw64
M       vbm12.man
M       vbm_vol_atlas.m
M       vbm_vol_downcut.mexmaci64
M       vbm_vol_downcut.mexw32
M       vbm_vol_downcut.mexw64
M       vbm_vol_eidist.mexglx
M       vbm_vol_eidist.mexmaci64
M       vbm_vol_eidist.mexw32
M       vbm_vol_eidist.mexw64
M       vbm_vol_eikonal3.mexmaci64
M       vbm_vol_eikonal3.mexw32
M       vbm_vol_eikonal3.mexw64
M       vbm_vol_genus0.mexa64
M       vbm_vol_genus0.mexglx
M       vbm_vol_genus0.mexmaci64
M       vbm_vol_genus0.mexw32
M       vbm_vol_genus0.mexw64
M       vbm_vol_gradient3.mexa64
M       vbm_vol_gradient3.mexglx
M       vbm_vol_gradient3.mexmaci64
M       vbm_vol_gradient3.mexw32
M       vbm_vol_gradient3.mexw64
M       vbm_vol_interp3f.mexmaci64
M       vbm_vol_interp3f.mexw32
M       vbm_vol_interp3f.mexw64
M       vbm_vol_laplace3.mexmaci64
M       vbm_vol_laplace3.mexw32
M       vbm_vol_laplace3.mexw64
M       vbm_vol_laplace3R.mexmaci64
M       vbm_vol_laplace3R.mexw32
M       vbm_vol_laplace3R.mexw64
M       vbm_vol_localstat.mexa64
M       vbm_vol_localstat.mexglx
M       vbm_vol_localstat.mexmaci64
M       vbm_vol_localstat.mexw32
M       vbm_vol_localstat.mexw64
M       vbm_vol_median3.mexmaci64
M       vbm_vol_median3.mexw32
M       vbm_vol_median3.mexw64
M       vbm_vol_median3c.mexmaci64
M       vbm_vol_median3c.mexw32
M       vbm_vol_median3c.mexw64
M       vbm_vol_pbtp.mexmaci64
M       vbm_vol_pbtp.mexw32
M       vbm_vol_pbtp.mexw64
M       vbm_vol_simgrow.mexmaci64
M       vbm_vol_simgrow.mexw32
M       vbm_vol_simgrow.mexw64

(1) Added new files to Makefile.vbm.
(2) Modified compile.m to consider different flags for different systems.
(3) Added ornlm files and adapted ornlmMex.c. Also changed to float format.
(4) Recompiled CAT and mexfiles.
(5) Corrected orientation of slices in cg_slice_overlay.m.

------------------------------------------------------------------------
r593 | dahnke | 2014-08-28 15:25:47 +0200 (Thu, 28 Aug 2014) | 24 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       ds.m
 M      templates_1.50mm
A       templates_1.50mm/Template_0_IXI555_MNI152.nii
A       templates_1.50mm/Template_1_IXI555_MNI152.nii
A       templates_1.50mm/Template_2_IXI555_MNI152.nii
A       templates_1.50mm/Template_3_IXI555_MNI152.nii
A       templates_1.50mm/Template_4_IXI555_MNI152.nii
A       templates_1.50mm/Template_5_IXI555_MNI152.nii
A       templates_1.50mm/Template_6_IXI555_MNI152.nii
M       vbm_io_writenii.m
M       vbm_surf_createCS.m
M       vbm_tst_pre.m

(1) Corrected GM segmentation error in the global intensity scaling process of
    PD/T2 images with strong underestimation of the GM segment.
(2) Optimized cerebellum LAS detection.
(3) Added "cleanupstr" variable.
(4) Corrected image x-axis properties by wrong boundary box values.
    Forced negative x-axis.
(5) Added "IXI555" template (x-axis properties update (4) is in process).

------------------------------------------------------------------------
r592 | dahnke | 2014-08-19 21:02:38 +0200 (Tue, 19 Aug 2014) | 25 lines

Changed paths:
 M      .
M       cg_vbm_defaults.m
M       cg_vbm_run_newcatch.m
M       cg_vbm_write.m
D       templates_1.50mm/TPM.nii
M       templates_1.50mm/aal.nii
M       templates_1.50mm/anatomy.csv
M       templates_1.50mm/anatomy.nii
M       templates_1.50mm/anatomy.txt
D       templates_1.50mm/brodmann.nii
M       templates_1.50mm/hammers.nii
M       templates_1.50mm/ibsr.nii
M       templates_1.50mm/mori.nii
M       templates_1.50mm/vbm12.nii
MM      vbm_check_system_output.m
M       vbm_vol_atlas.m
M       vbm_vol_partvol.m

(1) Corrected atlas image properties.
(2) Updated "anatomy" atlas (version 2.0).
(3) Removed "brodmann" atlas map due to missing labels.
(4) Removed "TPM.nii" from "template_1.50mm" directory.
(5) Updated "cg_vbm_default.m" parameters.

------------------------------------------------------------------------
r591 | dahnke | 2014-08-02 08:53:56 +0200 (Sat, 02 Aug 2014) | 103 lines

Changed paths:
 M      .
M       AmapMex.mexmaci64
M       cg_vbm_batch.m
M       cg_vbm_batch.sh
M       cg_vbm_defaults.m
M       cg_vbm_run.m
A       cg_vbm_run_job.m
A       cg_vbm_run_newcatch.m
A       cg_vbm_run_oldcatch.m
M       cg_vbm_write.m
M       compile.m
M       distribute_to_server.sh
A       ornlmMex.c
A       ornlmMex.m
A       ornlmMex.mexa64
A       ornlmMex.mexglx
A       ornlmMex.mexmaci
A       ornlmMex.mexmaci64
A       ornlmMex.mexw32
A       ornlmMex.mexw64
M       sanlmMex.mexmaci64
M       sanlmMex_noopenmp.mexmaci64
M       tbx_cfg_vbm.m
M       vbdist.mexmaci64
M       vbm_io_FreeSurfer.m
M       vbm_io_cmd.m
M       vbm_io_cprintf.m
M       vbm_stat_marks.m
M       vbm_stat_nanmean.m
M       vbm_stat_nanmedian.m
M       vbm_stat_nanstd.m
M       vbm_stat_nansum.m
M       vbm_surf_createCS.m
M       vbm_tst_SRS.m
M       vbm_tst_calc_kappa.m
M       vbm_tst_pre.m
M       vbm_tst_qa.m
M       vbm_vol_downcut.mexmaci64
M       vbm_vol_eidist.mexmaci64
M       vbm_vol_eikonal3.c
M       vbm_vol_eikonal3.mexmaci64
M       vbm_vol_genus0.mexmaci64
M       vbm_vol_gradient3.mexw32
M       vbm_vol_gradient3.mexw64
M       vbm_vol_interp3f.mexmaci64
M       vbm_vol_laplace3.mexmaci64
M       vbm_vol_laplace3R.mexmaci64
M       vbm_vol_localstat.c
M       vbm_vol_localstat.mexmaci64
M       vbm_vol_localstat.mexw32
M       vbm_vol_localstat.mexw64
M       vbm_vol_median3.mexmaci64
M       vbm_vol_median3c.mexmaci64
M       vbm_vol_morph.m
M       vbm_vol_partvol.m
M       vbm_vol_pbt.m
M       vbm_vol_pbtp.mexmaci64
M       vbm_vol_resize.m
M       vbm_vol_simgrow.mexmaci64

This update contain a lot of changes, corrections and updates for large parts of
the segmentation pipeline.
(1)  Added symbolic link support for "distribute_to_server.sh".
(2)  Optimized skull-stripping and removed "gcutcsf" parameter.
     Verified behavior of 'gcutstr' in range between 0 and 1.
(3)  Merged B3C inhomogeneity correction and the Local Adaptive Segmentation
     (LAS) with direct access to atlas data.
     Removed 'Final LAS corrections' and 'Final Masking' function and options.
     Verified behavior of 'LASstr' in range between 0 and 1.
(4)  Extended "BVC" to "BVCstr" parameter for further control of the blood
     vessel correction, with 0 for no correction.
     Verified behavior of 'BVCstr' in range between 0 and 1.
(5)  Updated and tested inverse pipeline 'extopts.INV' that is now part of the
     global intensity normalization function, including a small bias WM based
     inhomogeneity correction to avoid inversion problems.
     Verified behavior for T2 and PD datasets, with good results for good data.
(6)  Added new improved cleanup routine ('extopts.cleanup==3').
(7)  Added VBM warnings to 'vbm12*.mat' (QA.SW.vbm_warnings) and display them
     in the final report (not tested yet).
(8)  Added old ORNLM filter for noise removal after intensity scaling. The
     strength of the filter is controlled by a CJV like measure to assure
     smooth tissues. Using the NLM filter should work better than only a
     stronger MRF filter! Filter strength is limited by a sixth of tissue
     contrast.

Unsolved problems, warnings, and errors:
(1)  Unsolved errors for "extopts.kmeans=1" with AMAP segmentation errors.
(2)  Unsolved errors for surface generation "Cat_SeparatePolygon" or "reducepatch" under Windows with incorrect
     values of the vertices of the the surface faces.
(3)  Images with low NCR/high CNR trend to have local WM overestimation.
     The brainstem is a little bit to white and lead to WM overestimations in
     the cerebellum (see also BWP_MS2_Collins_t1_pn9_rf100pA.nii).
     > Check LAS bias correction.
(4)  To strong noise correction in high resolution images (ORNLM strength).
(5)  PD/T2 pipeline:
     > The GM/CSF boundary/peak estimation in low contrast images (CSF~GM)
       requires stronger connection of SPM-segmentation and intensity information
       (see XNAT-flash3 subjects / BWP_HC_Collins_pd_pn[3|9]_rf[040|100]pA ).
     > Some images show background inversion problems and requires blood vessel
       correction (NIH-T2 subjects).
     > Evaluation for IXI and NIH data in relation to T1 segmentation required

------------------------------------------------------------------------
r590 | gaser | 2014-07-24 12:37:56 +0200 (Thu, 24 Jul 2014) | 13 lines

Changed paths:
M       Makefile.vbm
M       cg_vbm_tools.m
M       spm_vbm12.m
M       vbm12.man
A       vbm_check_system_output.m
M       vbm_surf_createCS.m
M       vbm_surf_resamp.m

(1) Added function to resample and smooth existing freesurfer data.
(2) Added vbm_check_system_output.m that was used internally in several
    function that use system calls.

------------------------------------------------------------------------
r589 | dahnke | 2014-06-23 10:00:35 +0200 (Mon, 23 Jun 2014) | 42 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_tools.m
M       cg_vbm_write.m
M       checkinopt.m
M       spm_vbm12.m
M       vbm_io_colormaps.m
M       vbm_io_cprintf.m
A       vbm_io_struct2table.m
M       vbm_io_updateStruct.m
M       vbm_io_writenii.m
M       vbm_io_xml.m
A       vbm_io_xml2csv.m
M       vbm_plot_boxplot.m
M       vbm_qa_calcSTC.m
M       vbm_stat_marks.m
A       vbm_stat_nansum.m
A       vbm_tst_CJV.m
M       vbm_tst_SRS.m
M       vbm_tst_calc_kappa.m
M       vbm_tst_pre.m
A       vbm_tst_qa.m
M       vbm_tst_qa_groups.m
M       vbm_tst_qa_groups_test.m
D       vbm_tst_t1qa.m
M       vbm_vol_average.m
M       vbm_vol_gradient3.c
M       vbm_vol_gradient3.mexmaci64
M       vbm_vol_localstat.c
M       vbm_vol_localstat.mexmaci64
M       vbm_vol_morph.m
M       vbm_vol_partvol.m
D       vbm_vol_t1qacalc.m

(1)  Enhancement of opt-input structure of 'vbm_plot_boxplot', with coloring,
     different scalings, and outlier output. Requires further test!
(2)  Added PID output for Matlab calls of 'cg_vbm_batch.sh'.
(3)  Enhancement of 'vbm_tst_t1qa' with GUI and command line control in one file.
(4)  Corrected side error of warped images.
(5)  Update of 'vbm_io_structUpdate'.


------------------------------------------------------------------------
r588 | gaser | 2014-06-18 11:33:45 +0200 (Wed, 18 Jun 2014) | 61 lines

Changed paths:
M       AmapMex.mexmaci64
M       AmapMex.mexw32
M       AmapMex.mexw64
M       cg_check_cov.m
M       compile.m
M       sanlmMex.mexmaci64
M       sanlmMex.mexw32
M       sanlmMex.mexw64
M       sanlmMex_noopenmp.mexmaci64
M       sanlmMex_noopenmp.mexw32
M       sanlmMex_noopenmp.mexw64
!       templates_1.50mm/hammers.nii
M       vbdist.mexmaci64
M       vbdist.mexw32
M       vbdist.mexw64
M       vbm_vol_downcut.mexmaci64
M       vbm_vol_downcut.mexw32
M       vbm_vol_downcut.mexw64
M       vbm_vol_eidist.mexmaci64
M       vbm_vol_eidist.mexw32
M       vbm_vol_eidist.mexw64
M       vbm_vol_eikonal3.mexmaci64
M       vbm_vol_eikonal3.mexw32
M       vbm_vol_eikonal3.mexw64
M       vbm_vol_genus0.c
M       vbm_vol_genus0.mexmaci64
M       vbm_vol_genus0.mexw32
M       vbm_vol_genus0.mexw64
M       vbm_vol_gradient3.mexmaci64
M       vbm_vol_gradient3.mexw32
M       vbm_vol_gradient3.mexw64
M       vbm_vol_interp3f.mexmaci64
M       vbm_vol_interp3f.mexw32
M       vbm_vol_interp3f.mexw64
M       vbm_vol_laplace3.mexmaci64
M       vbm_vol_laplace3.mexw32
M       vbm_vol_laplace3.mexw64
M       vbm_vol_laplace3R.mexmaci64
M       vbm_vol_laplace3R.mexw32
M       vbm_vol_laplace3R.mexw64
M       vbm_vol_localstat.mexmaci64
M       vbm_vol_localstat.mexw32
M       vbm_vol_localstat.mexw64
M       vbm_vol_median3.mexmaci64
M       vbm_vol_median3.mexw32
M       vbm_vol_median3.mexw64
M       vbm_vol_median3c.mexmaci64
M       vbm_vol_median3c.mexw32
M       vbm_vol_median3c.mexw64
M       vbm_vol_pbtp.mexmaci64
M       vbm_vol_pbtp.mexw32
M       vbm_vol_pbtp.mexw64
M       vbm_vol_simgrow.mexmaci64
M       vbm_vol_simgrow.mexw32
M       vbm_vol_simgrow.mexw64

(1) Added additional flag to vbm_vol_genus0.c in order to allow simple
    surface extraction without volume-based topology correction.
(2) Recompiled windows and mac mex-files.

------------------------------------------------------------------------
r587 | gaser | 2014-03-21 10:12:52 +0100 (Fri, 21 Mar 2014) | 10 lines

Changed paths:
M       spm_vbm12.m
M       vbm_spm.m
M       vbm_vol_partvol.m

(1) vbm_vol_parts: flipping of sites to correct for wrong hemis (quick &
    dirty solution suggested by Robert).
(2) Vertices and faces are removed in vbm_spm.m to get rid of the huge
    SPM.mat files.

------------------------------------------------------------------------
r586 | gaser | 2014-03-18 17:29:41 +0100 (Tue, 18 Mar 2014) | 6 lines

Changed paths:
M       cg_check_cov.m

Some corrections and new functionality in cg_check_cov.m


------------------------------------------------------------------------
r585 | gaser | 2014-03-14 10:25:51 +0100 (Fri, 14 Mar 2014) | 7 lines

Changed paths:
M       cg_check_cov.m
M       spm_vbm12.m

(1) cg_check_cov now allows same scaling for all texture maps.
(2) Display surfaces can now display multiple surfaces.

------------------------------------------------------------------------
r584 | gaser | 2014-03-12 17:59:22 +0100 (Wed, 12 Mar 2014) | 5 lines

Changed paths:
M       vbm_surf_resamp.m

Corrected error in vbm_surf_resamp.m

------------------------------------------------------------------------
r583 | gaser | 2014-03-12 08:46:26 +0100 (Wed, 12 Mar 2014) | 24 lines

Changed paths:
M       AmapMex.mexw64
M       sanlmMex.mexw64
M       sanlmMex_noopenmp.mexw64
M       vbdist.mexw64
M       vbm12.man
M       vbm_surf_createCS.m
M       vbm_vol_downcut.mexw64
M       vbm_vol_eidist.mexw64
M       vbm_vol_eikonal3.mexw64
M       vbm_vol_genus0.mexw64
M       vbm_vol_gradient3.mexw64
M       vbm_vol_interp3f.mexw64
M       vbm_vol_laplace3.mexw64
M       vbm_vol_laplace3R.mexw64
M       vbm_vol_localstat.mexw64
M       vbm_vol_median3.mexw64
M       vbm_vol_median3c.mexw64
M       vbm_vol_pbtp.mexw64
M       vbm_vol_simgrow.mexw64

(1) Recompiled for Windows 64 bit.
(2) Error and catch handling in vbm_surf_create.m changed.

------------------------------------------------------------------------
r582 | gaser | 2014-03-11 16:42:00 +0100 (Tue, 11 Mar 2014) | 22 lines

Changed paths:
M       AmapMex.mexw32
M       sanlmMex.mexw32
M       sanlmMex_noopenmp.mexw32
M       vbdist.mexw32
M       vbm_vol_ctype.m
M       vbm_vol_downcut.mexw32
M       vbm_vol_eidist.mexw32
M       vbm_vol_eikonal3.mexw32
M       vbm_vol_genus0.mexw32
M       vbm_vol_gradient3.mexw32
M       vbm_vol_interp3f.mexw32
M       vbm_vol_laplace3.mexw32
M       vbm_vol_laplace3R.mexw32
M       vbm_vol_localstat.mexw32
M       vbm_vol_median3.mexw32
M       vbm_vol_median3c.mexw32
M       vbm_vol_pbtp.mexw32
M       vbm_vol_simgrow.mexw32

Changed order of inputs for strfind in vbm_vol_ctype.m.

------------------------------------------------------------------------
r581 | gaser | 2014-03-10 14:22:41 +0100 (Mon, 10 Mar 2014) | 6 lines

Changed paths:
M       vbm_surf_resamp.m

Surfaces are now resampled using sphere, while values will be still resampled
using sphere.reg.

------------------------------------------------------------------------
r580 | gaser | 2014-03-10 11:41:03 +0100 (Mon, 10 Mar 2014) | 7 lines

Changed paths:
M       cg_vbm_defaults.m
M       vbm_surf_createCS.m

(1) Deselected lesion mapping as default.
(2) Commented out set of NaN for CC and other areas in thickness maps.

------------------------------------------------------------------------
r579 | gaser | 2014-03-10 09:45:41 +0100 (Mon, 10 Mar 2014) | 6 lines

Changed paths:
M       vbm12.man
M       vbm_vol_ctype.m

vbm_vol_ctype.m can now work with datatypes such uint8-le.

------------------------------------------------------------------------
r578 | gaser | 2014-03-06 13:00:17 +0100 (Thu, 06 Mar 2014) | 10 lines

Changed paths:
M       cg_set_com.m
M       vbm_vol_localstat.mexa64
M       vbm_vol_localstat.mexglx
M       vbm_vol_localstat.mexw32
M       vbm_vol_localstat.mexw64

(1) Changed reference origin in cg_set_com.m for z-axis.
(2) Recompiled vbm_vol_localstat.c for all systems.

------------------------------------------------------------------------
r577 | dahnke | 2014-03-06 11:14:10 +0100 (Thu, 06 Mar 2014) | 38 lines

Changed paths:
M       cg_set_com.m
M       cg_vbm_batch.sh
M       cg_vbm_write.m
M       distribute_to_server.sh
M       templates_1.50mm/vbm12.nii
A       vbm_io_3Dto4D.m
M       vbm_io_colormaps.m
M       vbm_io_cprintf.m
M       vbm_io_remat.m
M       vbm_plot_boxplot.m
A       vbm_qa_calcSTC.m
M       vbm_stat_marks.m
M       vbm_surf_createCS.m
M       vbm_tst_calc_kappa.m
M       vbm_tst_pre.m
M       vbm_tst_t1qa.m
M       vbm_vol_atlas.m
M       vbm_vol_average.m
A       vbm_vol_ctype.m
M       vbm_vol_iscale.m
M       vbm_vol_localstat.c
M       vbm_vol_localstat.mexmaci64
M       vbm_vol_partvol.m

(1)  Force a stronger separation of new preprocessing routings from the well
     known stable routines by the "vbm.extopts.LAS" parameter, with 0 for the
     conservative pipeline (VBM12), and 1 for the version with new segmentation
     routines like B3C, LAS, WMHC, BVC, etc (VBM12i).
(2)  Corrected an error in vbm_vol_localstat, but this function still requires
     a major update for nan, inf, and zero behavior!
(3)  Updates for distributed processing of other MATLAB/SPM/VBM function in
     "cg_vbm_batch.sh" (and "distribute_to_server.sh").
(4)  Updated QA routines.
(5)  Set cut regions as NaN for cortical thickness map!
     This may lead to smoothing problems!


------------------------------------------------------------------------
r576 | gaser | 2014-03-03 15:24:39 +0100 (Mon, 03 Mar 2014) | 6 lines

Changed paths:
M       distribute_to_server.sh
M       vbm12.man

Some small changes to dsitribute_to_server.sh.

------------------------------------------------------------------------
r575 | gaser | 2014-03-03 12:56:38 +0100 (Mon, 03 Mar 2014) | 6 lines

Changed paths:
M       cg_vbm_defs.m

(1) Removed dependence on HDW toolbox in cg_vbm_defs.m
(2) Corrected wrong CAT.win32 folder to CAT.w32.

------------------------------------------------------------------------
r574 | dahnke | 2014-02-11 14:40:18 +0100 (Tue, 11 Feb 2014) | 13 lines

Changed paths:
M       cg_vbm_write.m
M       ds.m
M       templates_1.50mm/vbm12.nii
M       vbm_io_cprintf.m
M       vbm_vol_atlas.m
M       vbm_vol_partvol.m
M       vbm_vol_sanlm.m
M       vbm_vol_t1qacalc.m

(1)  Corrected small errors.
(2)  Corrected vbm12.nii atlas (side error).

------------------------------------------------------------------------
r573 | gaser | 2014-02-10 17:59:39 +0100 (Mon, 10 Feb 2014) | 7 lines

Changed paths:
M       cg_vbm_batch.m
M       cg_vbm_write.m

(1) Matlab R2007a does not accept catch err in cg_vbm_write.m
(2) Changed hamdling of rmfield in cg_vbm_batch.m

------------------------------------------------------------------------
r572 | gaser | 2014-02-10 11:09:48 +0100 (Mon, 10 Feb 2014) | 11 lines

Changed paths:
M       cg_vbm_write.m
M       vbm12.man
M       vbm_vol_atlas.m
M       vbm_vol_morph.m
M       vbm_vol_partvol.m
M       vbm_vol_pbt.m
M       vbm_vol_t1qacalc.m

Matlab R2007a does not accept terms such as [~,m] = function.

------------------------------------------------------------------------
r571 | gaser | 2014-02-10 10:52:24 +0100 (Mon, 10 Feb 2014) | 6 lines

Changed paths:
M       tbx_cfg_vbm.m
M       vbm12.man

removed too li,iting ufilter in tbx_cfg_vbm.m.

------------------------------------------------------------------------
r570 | gaser | 2014-02-07 11:01:45 +0100 (Fri, 07 Feb 2014) | 6 lines

Changed paths:
M       cg_vbm_batch.m
 M      templates_1.50mm/vbm12.nii

Corrected wrong handling of WMH in cg_vbm_batch.m.

------------------------------------------------------------------------
r569 | gaser | 2014-02-07 10:45:58 +0100 (Fri, 07 Feb 2014) | 48 lines

Changed paths:
M       AmapMex.mexw32
M       AmapMex.mexw64
M       cg_check_cov.m
M       distribute_to_server.sh
M       sanlmMex.mexw32
M       sanlmMex.mexw64
M       sanlmMex_noopenmp.mexw32
M       sanlmMex_noopenmp.mexw64
M       vbdist.mexw32
M       vbdist.mexw64
M       vbm12.man
M       vbm_vol_downcut.mexw32
M       vbm_vol_downcut.mexw64
M       vbm_vol_eidist.c
M       vbm_vol_eidist.mexa64
M       vbm_vol_eidist.mexmaci64
M       vbm_vol_eidist.mexw32
M       vbm_vol_eidist.mexw64
M       vbm_vol_eikonal3.mexw32
M       vbm_vol_eikonal3.mexw64
M       vbm_vol_genus0.mexw32
M       vbm_vol_genus0.mexw64
M       vbm_vol_gradient3.mexw32
M       vbm_vol_gradient3.mexw64
M       vbm_vol_interp3f.mexw32
M       vbm_vol_interp3f.mexw64
M       vbm_vol_laplace3.mexw32
M       vbm_vol_laplace3.mexw64
M       vbm_vol_laplace3R.mexw32
M       vbm_vol_laplace3R.mexw64
M       vbm_vol_localstat.mexw32
M       vbm_vol_localstat.mexw64
M       vbm_vol_median3.mexw32
M       vbm_vol_median3.mexw64
M       vbm_vol_median3c.mexw32
M       vbm_vol_median3c.mexw64
M       vbm_vol_pbtp.mexw32
M       vbm_vol_pbtp.mexw64
M       vbm_vol_simgrow.mexw32
M       vbm_vol_simgrow.mexw64

(1) Changed default definition of SUER in distribute_to_server.sh that worked
    not properly.
(2) Some slight changes in cg_check_cov.m.
(3) Changed vbm_vol_eidist.c according to standard gcc.
(4) Recompiled mexfiles.

------------------------------------------------------------------------
r568 | dahnke | 2014-02-06 18:40:18 +0100 (Thu, 06 Feb 2014) | 24 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       distribute_to_server.sh
A       templates_1.50mm/vbm12.nii
M       vbm_surf_createCS.m
M       vbm_tst_calc_kappa.m
M       vbm_tst_pre.m
M       vbm_tst_qa_groups.m
M       vbm_tst_qa_groups_test.m
M       vbm_tst_t1qa.m
M       vbm_vol_atlas.m
M       vbm_vol_eidist.c
M       vbm_vol_eidist.mexmaci64
M       vbm_vol_laplace3R.c
M       vbm_vol_partvol.m
M       vbm_vol_pbt.m

(1)  Corrected vbm_vol_eidist distance estimation.
(2)  Updated vbm_vol_pbt thickness estimation.
(3)  Added vbm12.nii region atlas that based on Hammers and replace the l1A atlas.
(4)  Updated ventricle and WMH partitioning by Laplace approach.
(5)  Update CSF global threshold estimation for high GM/WM-contrast images.

------------------------------------------------------------------------
r567 | gaser | 2014-01-27 16:24:56 +0100 (Mon, 27 Jan 2014) | 7 lines

Changed paths:
M       cg_check_cov.m
M       cg_vbm_defaults.m
M       vbm12.man

Some minor changes to cg_check_cov.m.

------------------------------------------------------------------------
r566 | gaser | 2014-01-27 12:48:22 +0100 (Mon, 27 Jan 2014) | 5 lines

Changed paths:
M       vbm_vol_eidist.mexmaci64

Removed debugging output in vbm_vol_eidist.c

------------------------------------------------------------------------
r565 | gaser | 2014-01-27 12:44:05 +0100 (Mon, 27 Jan 2014) | 6 lines

Changed paths:
M       cg_vbm_batch.m
M       cg_vbm_tools.m

Some changes in cg_vbm_tools.m and cg_vbm_batch.m to use batch mode.

------------------------------------------------------------------------
r564 | gaser | 2014-01-27 11:25:19 +0100 (Mon, 27 Jan 2014) | 6 lines

Changed paths:
M       Makefile.vbm
M       vbm12.man

Removed cg_check_mesh_cov from Makefile.vbm.

------------------------------------------------------------------------
r563 | gaser | 2014-01-27 11:22:36 +0100 (Mon, 27 Jan 2014) | 6 lines

Changed paths:
 M      tricases.h
M       vbm12.man

Removed CAT.maci64 because of difficulties to use subversion for binaries.

------------------------------------------------------------------------
r562 | gaser | 2014-01-27 11:18:54 +0100 (Mon, 27 Jan 2014) | 4 lines

Changed paths:

Removed CAT.maci64 because of difficulties to use subversion for binaries.

------------------------------------------------------------------------
r561 | gaser | 2014-01-27 11:16:21 +0100 (Mon, 27 Jan 2014) | 6 lines

Changed paths:
A       tricases.h
M       vbm12.man

Added missing tricases.h.

------------------------------------------------------------------------
r560 | gaser | 2014-01-27 11:14:49 +0100 (Mon, 27 Jan 2014) | 9 lines

Changed paths:
 M      vbm_vol_genus0.mexa64
 M      vbm_vol_genus0.mexglx
 M      vbm_vol_genus0.mexmaci64
 M      vbm_vol_genus0.mexw32
 M      vbm_vol_genus0.mexw64

Added missing vbm_vol_genus0.mex* files.

------------------------------------------------------------------------
r559 | gaser | 2014-01-27 11:14:36 +0100 (Mon, 27 Jan 2014) | 9 lines

Changed paths:
 M      fsaverage/fsavg.index2D_256x128.txt
 M      genus0.c
 M      genus0.h
M       vbm12.man
MM      vbm_vol_genus0.c

Added missing vbm_vol_genus0.mex* files.

------------------------------------------------------------------------
r558 | gaser | 2014-01-27 11:14:05 +0100 (Mon, 27 Jan 2014) | 9 lines

Changed paths:
A       vbm_vol_genus0.mexa64
A       vbm_vol_genus0.mexglx
A       vbm_vol_genus0.mexmaci64
A       vbm_vol_genus0.mexw32
A       vbm_vol_genus0.mexw64

Added missing vbm_vol_genus0.mex* files.

------------------------------------------------------------------------
r557 | gaser | 2014-01-27 11:12:51 +0100 (Mon, 27 Jan 2014) | 107 lines

Changed paths:
M       AmapMex.mexa64
M       AmapMex.mexglx
M       AmapMex.mexmaci64
M       AmapMex.mexw32
M       AmapMex.mexw64
M       Kmeans.c
M       Makefile.vbm
M       cg_check_cov.m
D       cg_check_mesh_cov.m
M       cg_vbm_tools.m
M       cg_vbm_write.m
M       compile.m
A       fsaverage/fsavg.index2D_256x128.txt
A       genus0.c
A       genus0.h
M       sanlmMex.mexglx
M       sanlmMex.mexmaci64
M       sanlmMex.mexw32
M       sanlmMex.mexw64
M       sanlmMex_noopenmp.mexmaci64
M       sanlmMex_noopenmp.mexw32
M       sanlmMex_noopenmp.mexw64
M       spm_vbm12.m
M       vbdist.c
M       vbdist.mexa64
M       vbdist.mexglx
M       vbdist.mexmaci64
M       vbdist.mexw32
M       vbdist.mexw64
M       vbm12.man
M       vbm_surf_createCS.m
M       vbm_vol_downcut.c
M       vbm_vol_downcut.mexa64
M       vbm_vol_downcut.mexglx
M       vbm_vol_downcut.mexmaci64
M       vbm_vol_downcut.mexw32
M       vbm_vol_downcut.mexw64
M       vbm_vol_eidist.c
M       vbm_vol_eidist.mexa64
M       vbm_vol_eidist.mexglx
M       vbm_vol_eidist.mexmaci64
M       vbm_vol_eidist.mexw32
M       vbm_vol_eidist.mexw64
M       vbm_vol_eikonal3.c
M       vbm_vol_eikonal3.mexa64
M       vbm_vol_eikonal3.mexglx
M       vbm_vol_eikonal3.mexmaci64
M       vbm_vol_eikonal3.mexw32
M       vbm_vol_eikonal3.mexw64
A       vbm_vol_genus0.c
M       vbm_vol_gradient3.mexmaci64
M       vbm_vol_gradient3.mexw32
M       vbm_vol_gradient3.mexw64
M       vbm_vol_interp3f.mexmaci64
M       vbm_vol_interp3f.mexw32
M       vbm_vol_interp3f.mexw64
M       vbm_vol_laplace3.mexmaci64
M       vbm_vol_laplace3.mexw32
M       vbm_vol_laplace3.mexw64
M       vbm_vol_laplace3R.mexmaci64
M       vbm_vol_laplace3R.mexw32
M       vbm_vol_laplace3R.mexw64
M       vbm_vol_localstat.c
M       vbm_vol_localstat.mexa64
M       vbm_vol_localstat.mexglx
M       vbm_vol_localstat.mexmaci64
M       vbm_vol_localstat.mexw32
M       vbm_vol_localstat.mexw64
M       vbm_vol_median3.c
M       vbm_vol_median3.mexa64
M       vbm_vol_median3.mexglx
M       vbm_vol_median3.mexmaci64
M       vbm_vol_median3.mexw32
M       vbm_vol_median3.mexw64
M       vbm_vol_median3c.c
M       vbm_vol_median3c.mexa64
M       vbm_vol_median3c.mexglx
M       vbm_vol_median3c.mexmaci64
M       vbm_vol_median3c.mexw32
M       vbm_vol_median3c.mexw64
M       vbm_vol_pbtp.cpp
M       vbm_vol_pbtp.mexa64
M       vbm_vol_pbtp.mexglx
M       vbm_vol_pbtp.mexmaci64
M       vbm_vol_pbtp.mexw32
M       vbm_vol_pbtp.mexw64
M       vbm_vol_simgrow.mexa64
M       vbm_vol_simgrow.mexglx
M       vbm_vol_simgrow.mexmaci64
M       vbm_vol_simgrow.mexw32
M       vbm_vol_simgrow.mexw64

(1) Corrected typos in vbm_vol_downcut.c, Kmeans.c, genus0.c.
(2) Added vbm_vol_genus0.c and genus0.*
(3) Replaced isosurface in vbm_surf_createCS.m by vbm_vol_genus0.
(4) Added missing extension ee in vbm_surf_createCS.m.
(5) Changed compile.m and Makefile.vbm to consider new files.
(6) Recompiled mexfiles for all systems.
(8) Updated cg_check_cov.m that can now deal with volume and surface data.
(9) Deleted cg_check_mesh_cov.m that is replaced by cg_check_cov.m.
(10) Updated cg_vbm_tools.m and spm_vbm12.m for new cg_check_cov.m.
(11) Added fsaverage/fsavg.index2D_256x128.txt (index for 2D map).
(12) Redefined FNAN and FINFINITY in vol_vol_edist.c to work with MSC.



------------------------------------------------------------------------
r556 | dahnke | 2014-01-23 09:36:10 +0100 (Thu, 23 Jan 2014) | 22 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       ds.m
M       tbx_cfg_vbm.m
M       vbm_io_writenii.m
M       vbm_tst_calc_kappa.m
M       vbm_tst_pre.m
M       vbm_vol_ROIval.c
M       vbm_vol_downcut.c
M       vbm_vol_eidist.c
MM      vbm_vol_eidist.mexmaci64
M       vbm_vol_iscale.m
M       vbm_vol_localstat.c
M       vbm_vol_partvol.m

(1)   Corrected intensity scaling problem for images with non-zero background
      (BWP MS case).
(2)   Corrected eidist.c error.



------------------------------------------------------------------------
r555 | gaser | 2014-01-10 12:43:11 +0100 (Fri, 10 Jan 2014) | 10 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       spm_vbm12.m
M       vbm12.man

(1) Removed saving of temporary file in cg_vbm_write.m.
(2) Don't write label as default.
(3) Removed option for longitudinal data, because this is not yet prepared.

------------------------------------------------------------------------
r554 | dahnke | 2014-01-08 17:27:53 +0100 (Wed, 08 Jan 2014) | 11 lines

Changed paths:
M       cg_vbm_write.m
M       vbm_stat_nanmean.m
M       vbm_stat_nanstd.m
M       vbm_surf_createCS.m
M       vbm_tst_pre.m
 M      vbm_vol_ROIval.mexmaci64
RM      vbm_vol_eidist.mexmaci64

Corrected minor errors.

------------------------------------------------------------------------
r553 | dahnke | 2013-12-21 19:50:22 +0100 (Sat, 21 Dec 2013) | 27 lines

Changed paths:
 M      .
M       CHANGES.txt
M       cg_vbm_batch.m
M       cg_vbm_defaults.m
M       cg_vbm_write.m
 M      fsaverage/lh.central
 M      fsaverage/lh.central.gii
 M      fsaverage/rh.central
 M      fsaverage/rh.central.gii
M       sanlmMex.mexmaci64
M       vbm_io_cmd.m
M       vbm_io_cprintf.m
M       vbm_surf_createCS.m
M       vbm_tst_pre.m
M       vbm_vol_ROIval.c
A       vbm_vol_ROIval.mexmaci64
M       vbm_vol_partvol.m
M       vbm_vol_pbt.m

(1)  Updated cmd line plot (vbm_vol_cmd) for detailed output (vbm.extopts.verb)
     of the partitioning (vbm_vol_partvol), the skull-stripping (vbm_vol_gcut2
     in cg_write_vol), and the ROI estimation.
(2)  Updated partition and skull-stripping functions. Removed errors and inc.
     calculation speed. Add resolution variable (vbm.extopts.vx_res), where
     images with higher resolutions are reduce to the half resolution.

------------------------------------------------------------------------
r552 | gaser | 2013-12-18 17:24:50 +0100 (Wed, 18 Dec 2013) | 17 lines

Changed paths:
A       fsaverage/lh.central
A       fsaverage/lh.central.gii
D       fsaverage/lh.smoothwm
D       fsaverage/lh.smoothwm.gii
A       fsaverage/rh.central
A       fsaverage/rh.central.gii
D       fsaverage/rh.smoothwm
D       fsaverage/rh.smoothwm.gii
 M      sanlmMex_noopenmp.mexw32
 M      sanlmMex_noopenmp.mexw64
M       spm_vbm12.m
M       vbm_spm.m
M       vbm_surf_createCS.m

Changed template from smoothwm to central surface and changed code resp.

------------------------------------------------------------------------
r551 | gaser | 2013-12-12 17:41:13 +0100 (Thu, 12 Dec 2013) | 7 lines

Changed paths:
M       cg_vbm_write.m
M       vbm_surf_resamp.m

Calculation of parameter Ycls was done for each slice leading to long
computation time in cg_vbm_write.m.

------------------------------------------------------------------------
r550 | gaser | 2013-12-12 14:30:58 +0100 (Thu, 12 Dec 2013) | 9 lines

Changed paths:
A       fsaverage/lh.smoothwm.gii
A       fsaverage/rh.smoothwm.gii
A       sanlmMex_noopenmp.mexw32
A       sanlmMex_noopenmp.mexw64

(1) Added gifti files for fsaverage surfaces.
(2) Added missing sanlmMex_noopenmp.mexw* files for windows.

------------------------------------------------------------------------
r549 | gaser | 2013-12-12 14:25:54 +0100 (Thu, 12 Dec 2013) | 16 lines

Changed paths:
D       AmapMex.mexmaci
M       Makefile.vbm
 M      cg_boxplot.m
MM      cg_check_mesh_cov.m
D       sanlmMex.mexmaci
D       sanlmMex_noopenmp.mexmaci
D       spm_def2det.mexmaci
D       vbdist.mexmaci
M       vbm12.man
M       vbm_surf_createCS.m
M       vbm_surf_resamp.m

(1) Removed old *mexmaci files (that were not complete at all).
(2) Some cosmetic changes to vbm_surf_createCS.m and vbm_surf_resample.m

------------------------------------------------------------------------
r548 | dahnke | 2013-12-12 12:22:20 +0100 (Thu, 12 Dec 2013) | 37 lines

Changed paths:
 M      .
M       cg_vbm_defaults.m
M       cg_vbm_run.m
M       cg_vbm_write.m
D       dp.m
A       vbm_io_cmd.m
M       vbm_io_cprintf.m
M       vbm_stat_nanmean.m
M       vbm_stat_nanstd.m
M       vbm_surf_createCS.m
M       vbm_tst_pre.m
D       vbm_vol_GBM.m
A       vbm_vol_ROIval.c
M       vbm_vol_iscale.m
M       vbm_vol_morph.m
M       vbm_vol_partvol.m
M       vbm_vol_pbt.m

(1)  Updated error handling:
      (a) If surface estimation failed on c-functions (segmenation error) VBM
          will not crash and only print an error message and go on with further
          VBM preprocessing.
      (b) Further error handling for VBM errors (delete temporary files that are
          not used for error diagnosis).
(2)  Made vbm_io_cmd to a separate function.
(3)  WM hyperintensity correction (extopts.WMHC) is ready for alpha tests.
     Estimation of WMHs based on the GM next to the ventricle that do not belong
     to the basal ganglia. Therefore, errors are often related to errors of the
     partitioning of these regions.
(4)  Major update of vbm_vol_partvol with simpler structure, higher speed and
     more comments.
(5)  Corrected error in vbm_vol_morph.
(6)  Restored full function of "finalmasking" and "cleanup" also for LAS.
     Removed old skull-stripping (vbm_vol_GBM).
(7)  Corrected error for global intensity Normalization for BG=CSF case.

------------------------------------------------------------------------
r547 | gaser | 2013-12-12 11:36:52 +0100 (Thu, 12 Dec 2013) | 6 lines

Changed paths:
M       cg_check_mesh_cov.m
MM      vbm_spm.m

Some rather cosmetic changes to cg_check_mesh_render.m

------------------------------------------------------------------------
r546 | gaser | 2013-12-12 10:43:04 +0100 (Thu, 12 Dec 2013) | 34 lines

Changed paths:
M       AmapMex.mexmaci64
M       Makefile.vbm
A       cg_boxplot.m
M       cg_check_cov.m
A       cg_check_mesh_cov.m
M       cg_vbm_batch.m
M       cg_vbm_defaults.m
M       cg_vbm_tools.m
M       compile.m
M       sanlmMex.mexmaci64
M       sanlmMex_noopenmp.mexmaci64
M       spm_vbm12.m
M       vbdist.mexmaci64
M       vbm12.man
M       vbm_vol_downcut.mexmaci64
M       vbm_vol_eidist.mexmaci64
M       vbm_vol_eikonal3.mexmaci64
M       vbm_vol_gradient3.mexmaci64
M       vbm_vol_interp3f.mexmaci64
M       vbm_vol_laplace3.mexmaci64
M       vbm_vol_laplace3R.mexmaci64
M       vbm_vol_localstat.mexmaci64
M       vbm_vol_median3.mexmaci64
M       vbm_vol_median3c.mexmaci64
M       vbm_vol_pbtp.mexmaci64
M       vbm_vol_simgrow.mexmaci64

(1) Removed multi-thread support for sanlmMex because results differ and it's
    not working for OSX < 10.6.
(2) Compiled mex-files for OSX < 10.6.
(3) Added cg_check_mesh_cov.m to check surface covariance.
(4) Added cg_boxplot (extracted from cg_check_cov.m).

------------------------------------------------------------------------
r545 | gaser | 2013-12-11 17:26:30 +0100 (Wed, 11 Dec 2013) | 11 lines

Changed paths:
M       cg_vbm_run.m
M       spm_vbm12.m
A       vbm_spm.m

(1) Added vbm_spm for factorial design. This is a modified version
    of spm_spm.m where the underlaying surface is replaced with fsaverage
    and the smoothness estimation is modified.
(2) spm_vbm12 is now extended by factorial design function adn estimation.
(3) Remove sanlm-filtered image after cg_vbm_write.m

------------------------------------------------------------------------
r544 | gaser | 2013-12-11 16:15:09 +0100 (Wed, 11 Dec 2013) | 7 lines

Changed paths:
M       cg_vbm_tools.m
M       vbm_surf_parameters.m
M       vbm_surf_resamp.m

Corrected some small bugs in resampling code.

------------------------------------------------------------------------
r543 | gaser | 2013-12-11 15:51:05 +0100 (Wed, 11 Dec 2013) | 7 lines

Changed paths:
MM      distribute_to_server.sh
M       vbm_surf_createCS.m
M       vbm_surf_resamp.m

Topology artefacts/defets are now marked in a gifti file.

------------------------------------------------------------------------
r542 | gaser | 2013-12-11 14:49:40 +0100 (Wed, 11 Dec 2013) | 8 lines

Changed paths:
M       Makefile.vbm
M       distribute_to_server.sh
MM      vbm_surf_parameters.m
MM      vbm_surf_resamp.m

Some small changes in distribute_to_server.sh.

------------------------------------------------------------------------
r541 | gaser | 2013-12-11 14:31:30 +0100 (Wed, 11 Dec 2013) | 12 lines

Changed paths:
M       cg_vbm_batch.m
M       cg_vbm_batch.sh
A       distribute_to_server.sh
M       vbm12.man

(1) Made some small changes to batch mode.
(2) Added new script distribute_to_server.sh that allows to distribute jobs
    to other server machines. Furthermore all files in a folder can be processed
    by excluding those file wehre a prepending pattern can be found
    (e.g. m0wrp1),

------------------------------------------------------------------------
r540 | gaser | 2013-12-10 16:41:44 +0100 (Tue, 10 Dec 2013) | 10 lines

Changed paths:
M       cg_vbm_tools.m
M       cg_vbm_update.m
M       sanlm_float.c
M       spm_vbm12.m
A       vbm_surf_parameters.m
A       vbm_surf_resamp.m

Added surface functions for parameter extraction and resampling.

------------------------------------------------------------------------
r539 | gaser | 2013-12-10 09:28:06 +0100 (Tue, 10 Dec 2013) | 5 lines

Changed paths:

(1) Corrected wrong url in update function.
(2) Removed CAT binaries because of the annoying issues.

------------------------------------------------------------------------
r538 | gaser | 2013-12-10 09:26:52 +0100 (Tue, 10 Dec 2013) | 55 lines

Changed paths:
D       CAT.glnx86
D       CAT.glnx86/CAT_3dVol2Surf
D       CAT.glnx86/CAT_AddValuesToSurf
D       CAT.glnx86/CAT_BlurSurfHK
D       CAT.glnx86/CAT_DeformSurf
D       CAT.glnx86/CAT_DumpCurv
D       CAT.glnx86/CAT_DumpGI
D       CAT.glnx86/CAT_FixTopology
D       CAT.glnx86/CAT_FractalDimension
D       CAT.glnx86/CAT_Isometize
D       CAT.glnx86/CAT_LBConformalMap
D       CAT.glnx86/CAT_ResampleSphericalSurf
D       CAT.glnx86/CAT_ResampleSurf
D       CAT.glnx86/CAT_SeparatePolygon
D       CAT.glnx86/CAT_Surf2Sphere
D       CAT.glnx86/CAT_WarpSurf
D       CAT.maci64
D       CAT.maci64/CAT_3dVol2Surf
D       CAT.maci64/CAT_AddValuesToSurf
D       CAT.maci64/CAT_BlurSurfHK
D       CAT.maci64/CAT_DeformSurf
D       CAT.maci64/CAT_DumpCurv
D       CAT.maci64/CAT_DumpGI
D       CAT.maci64/CAT_FixTopology
D       CAT.maci64/CAT_FractalDimension
D       CAT.maci64/CAT_Isometize
D       CAT.maci64/CAT_LBConformalMap
D       CAT.maci64/CAT_ResampleSphericalSurf
D       CAT.maci64/CAT_ResampleSurf
D       CAT.maci64/CAT_SeparatePolygon
D       CAT.maci64/CAT_Surf2Sphere
D       CAT.maci64/CAT_WarpSurf
D       CAT.win32
D       CAT.win32/CAT_3dVol2Surf.exe
D       CAT.win32/CAT_AddValuesToSurf.exe
D       CAT.win32/CAT_BlurSurfHK.exe
D       CAT.win32/CAT_DeformSurf.exe
D       CAT.win32/CAT_DumpCurv.exe
D       CAT.win32/CAT_DumpGI.exe
D       CAT.win32/CAT_FixTopology.exe
D       CAT.win32/CAT_FractalDimension.exe
D       CAT.win32/CAT_Isometize.exe
D       CAT.win32/CAT_LBConformalMap.exe
D       CAT.win32/CAT_ResampleSphericalSurf.exe
D       CAT.win32/CAT_ResampleSurf.exe
D       CAT.win32/CAT_SeparatePolygon.exe
D       CAT.win32/CAT_Surf2Sphere.exe
D       CAT.win32/CAT_WarpSurf.exe
M       cg_vbm_update.m
M       vbm12.man

(1) Corrected wrong url in update function.
(2) Removed CAT binaries because of the annoying issues.

------------------------------------------------------------------------
r537 | gaser | 2013-12-09 20:07:39 +0100 (Mon, 09 Dec 2013) | 52 lines

Changed paths:
M       CAT.glnx86/CAT_3dVol2Surf
M       CAT.glnx86/CAT_AddValuesToSurf
M       CAT.glnx86/CAT_BlurSurfHK
M       CAT.glnx86/CAT_DeformSurf
M       CAT.glnx86/CAT_DumpCurv
M       CAT.glnx86/CAT_DumpGI
M       CAT.glnx86/CAT_FixTopology
M       CAT.glnx86/CAT_FractalDimension
M       CAT.glnx86/CAT_Isometize
M       CAT.glnx86/CAT_LBConformalMap
M       CAT.glnx86/CAT_ResampleSphericalSurf
M       CAT.glnx86/CAT_ResampleSurf
M       CAT.glnx86/CAT_SeparatePolygon
M       CAT.glnx86/CAT_Surf2Sphere
M       CAT.glnx86/CAT_WarpSurf
RM      CAT.maci64/CAT_3dVol2Surf
RM      CAT.maci64/CAT_AddValuesToSurf
RM      CAT.maci64/CAT_BlurSurfHK
RM      CAT.maci64/CAT_DeformSurf
RM      CAT.maci64/CAT_DumpCurv
RM      CAT.maci64/CAT_DumpGI
RM      CAT.maci64/CAT_FixTopology
RM      CAT.maci64/CAT_FractalDimension
RM      CAT.maci64/CAT_Isometize
RM      CAT.maci64/CAT_LBConformalMap
RM      CAT.maci64/CAT_ResampleSphericalSurf
RM      CAT.maci64/CAT_ResampleSurf
RM      CAT.maci64/CAT_SeparatePolygon
RM      CAT.maci64/CAT_Surf2Sphere
RM      CAT.maci64/CAT_WarpSurf
M       CAT.win32/CAT_3dVol2Surf.exe
M       CAT.win32/CAT_AddValuesToSurf.exe
M       CAT.win32/CAT_BlurSurfHK.exe
M       CAT.win32/CAT_DeformSurf.exe
M       CAT.win32/CAT_DumpCurv.exe
M       CAT.win32/CAT_DumpGI.exe
M       CAT.win32/CAT_FixTopology.exe
M       CAT.win32/CAT_FractalDimension.exe
M       CAT.win32/CAT_Isometize.exe
M       CAT.win32/CAT_LBConformalMap.exe
M       CAT.win32/CAT_ResampleSphericalSurf.exe
M       CAT.win32/CAT_ResampleSurf.exe
M       CAT.win32/CAT_SeparatePolygon.exe
M       CAT.win32/CAT_Surf2Sphere.exe
M       CAT.win32/CAT_WarpSurf.exe
M       CHANGES.txt
M       vbm_surf_createCS.m

(1) Added new binaries for all platforms.
(2) Corrected wrong path for linux binaries in vbm_surf_createCS.m.

------------------------------------------------------------------------
r536 | gaser | 2013-12-09 10:36:38 +0100 (Mon, 09 Dec 2013) | 16 lines

Changed paths:
M       CAT.maci64/CAT_BlurSurfHK
M       CAT.maci64/CAT_DumpCurv
M       CAT.maci64/CAT_DumpGI
M       CAT.maci64/CAT_FixTopology
M       CAT.maci64/CAT_FractalDimension
M       CAT.maci64/CAT_Isometize
M       CAT.maci64/CAT_LBConformalMap
M       CAT.maci64/CAT_ResampleSphericalSurf
M       CAT.maci64/CAT_ResampleSurf
M       CAT.maci64/CAT_Surf2Sphere
M       CAT.maci64/CAT_WarpSurf

New version of CAT_Surf2Sphere that can now deal with reducepatched
data.

------------------------------------------------------------------------
r535 | dahnke | 2013-12-04 18:51:36 +0100 (Wed, 04 Dec 2013) | 55 lines

Changed paths:
M       AmapMex.c
M       AmapMex.mexmaci64
M       CAT.maci64/CAT_FixTopology
M       cg_vbm_batch.m
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       tbx_cfg_vbm.m
M       vbm_plot_boxplot.m
A       vbm_stat_nanmean.m
A       vbm_stat_nanmedian.m
A       vbm_stat_nanstd.m
M       vbm_surf_createCS.m
M       vbm_tst_SRS.m
M       vbm_tst_calc_bias.m
M       vbm_tst_calc_kappa.m
M       vbm_tst_pre.m
M       vbm_tst_qa_groups.m
M       vbm_tst_staple_multilabels.m
M       vbm_tst_t1qa.m
M       vbm_vol_atlas.m
M       vbm_vol_average.m
M       vbm_vol_iscale.m
M       vbm_vol_nanmean3.m
M       vbm_vol_partvol.m
M       vbm_vol_resize.m
M       vbm_vol_smooth3X.m
M       vbm_vol_t1qacalc.m

(1)  Renamed 'vbm_*.ps' to 'vbmreport_*' for correct spm-sorting of filetypes.
(2)  Added experimental WM hyperintensity (WMH) correction (extopts.WMHC), WMH
     detection (vbm_vol_partioning) and WMH correction (in cg_write_vol).
     WARNING: This code is in a very early development step and do not work yet
              and default extopts.WMHC=0!
(3)  Added variable (extopts.gcutCSF) to modify the gcut+ skull-stripping to
     obtain more surrounding CSF.
     WARNING: CSF contrast depend strongly on the MR-protocol, and high contrast
              images may have a similar intensity of CSF, background and bone!
              Therefore CSF segment quality can vary strongly for multi-protocol
              VBM, and extopts.gcutCSF may be turned off!
              Added a warning for this case.
(4)  Updated mean tissue intensity estimation for global intensity correction.
(5)  Replaced MATLAB toolbox nan-functions and calls by own methods:
     vbm_stat_nanmean,vbm_stat_nanstd,vbm_stat_nanmedian
(6)  Created subfunctions for longer parts in cg_vbm_write to increase readability
     may with some cost of memory (but this should be no critical part):
      (a) the global intensity normalization (vbm_pre_gintnorm)
      (b) fast partitioning for major brain structures (vbm_pre_fastpart)
      (c) brain and maximum-based bias correction B3C (vbm_pre_B3C)
      (d) calc preprocessing expectation map (vbm_qa_calcTE)
(7)  Created subfunctions for often used parts in cg_vbm_write:
      (a) egde image Yg (vbm_vol_grad)
      (b) fast divergence image Ydiv (vbm_vol_div)
(8)  Corrected output for atlas, te, pc images in tbx_cfg_vbm and cg_vbm_batch.

------------------------------------------------------------------------
r534 | gaser | 2013-11-29 13:04:04 +0100 (Fri, 29 Nov 2013) | 26 lines

Changed paths:
M       CAT.maci64/CAT_3dVol2Surf
M       CAT.maci64/CAT_AddValuesToSurf
M       CAT.maci64/CAT_BlurSurfHK
M       CAT.maci64/CAT_DeformSurf
M       CAT.maci64/CAT_DumpCurv
M       CAT.maci64/CAT_DumpGI
M       CAT.maci64/CAT_FixTopology
M       CAT.maci64/CAT_FractalDimension
M       CAT.maci64/CAT_Isometize
M       CAT.maci64/CAT_LBConformalMap
M       CAT.maci64/CAT_ResampleSphericalSurf
M       CAT.maci64/CAT_ResampleSurf
M       CAT.maci64/CAT_SeparatePolygon
M       CAT.maci64/CAT_Surf2Sphere
M       CAT.maci64/CAT_WarpSurf
M       cg_vbm_batch.sh
M       cg_vbm_write.m
M       vbm_surf_createCS.m

(1) Many changes in cg_vbm_write to prevent division by zero and negative
    and floating values for uint8.
(2) Changed handling of error message inside try-catch (now with e=lasterror).
(3) Added smoothing parameter for CAT_BlurSurfHK in vbm_surf_createCS.m.
(4) Replaced some corrupt binaries for maci64.

------------------------------------------------------------------------
r533 | gaser | 2013-11-29 08:10:16 +0100 (Fri, 29 Nov 2013) | 5 lines

Changed paths:
M       CAT.maci64/CAT_FixTopology

Modified CAT_FixTopology.

------------------------------------------------------------------------
r532 | gaser | 2013-11-28 16:21:49 +0100 (Thu, 28 Nov 2013) | 37 lines

Changed paths:
M       AmapMex.mexmaci64
MM      CAT.maci64/CAT_3dVol2Surf
 M      CAT.maci64/CAT_AddValuesToSurf
 M      CAT.maci64/CAT_BlurSurfHK
 M      CAT.maci64/CAT_DeformSurf
 M      CAT.maci64/CAT_DumpCurv
 M      CAT.maci64/CAT_DumpGI
MM      CAT.maci64/CAT_FixTopology
MM      CAT.maci64/CAT_FractalDimension
MM      CAT.maci64/CAT_Isometize
 M      CAT.maci64/CAT_LBConformalMap
 M      CAT.maci64/CAT_ResampleSphericalSurf
 M      CAT.maci64/CAT_ResampleSurf
 M      CAT.maci64/CAT_SeparatePolygon
 M      CAT.maci64/CAT_Surf2Sphere
MM      CAT.maci64/CAT_WarpSurf
M       cg_vbm_write.m
M       sanlmMex.mexmaci64
M       vbdist.mexmaci64
M       vbm_surf_createCS.m
M       vbm_vol_downcut.mexmaci64
M       vbm_vol_eidist.mexmaci64
M       vbm_vol_eikonal3.mexmaci64
M       vbm_vol_gradient3.mexmaci64
M       vbm_vol_interp3f.mexmaci64
M       vbm_vol_laplace3.mexmaci64
M       vbm_vol_laplace3R.mexmaci64
M       vbm_vol_localstat.mexmaci64
M       vbm_vol_median3.mexmaci64
M       vbm_vol_median3c.mexmaci64
M       vbm_vol_pbtp.mexmaci64
M       vbm_vol_simgrow.mexmaci64

(1) Added subtle surface smoothing after topology correction.
(2) Removed bug in cg_vbm_write caused by nonexisting 'left' field.

------------------------------------------------------------------------
r531 | dahnke | 2013-11-27 18:47:09 +0100 (Wed, 27 Nov 2013) | 26 lines

Changed paths:
M       cg_vbm_batch.m
M       cg_vbm_defaults.m
M       cg_vbm_write.m
D       findfiles.m
M       tbx_cfg_vbm.m
M       vbm12.txt
M       vbm_db.m
A  +    vbm_findfiles.m
M       vbm_surf_createCS.m
M       vbm_tst_SRS.m
M       vbm_tst_pre.m
M       vbm_tst_qa_groups_test.m
M       vbm_tst_t1qa.m
M       vbm_vol_atlas.m
M       vbm_vol_pbt.m
M       vbm_vol_resize.m
M       vbm_vol_t1qacalc.m

(1)  Updated surface output names in 'cg_vbm_defaults-file'.
(2)  Changed function-name 'findfiles' to 'vbm_findfiles'.
(3)  Updated command line output of surface pipeline.
(4)  Added debugging parameter to 'cg_vbm_defaults'.
(5)  Added surface parameter to GUI.
(6)  Deactivated surface refinement due to position error.

------------------------------------------------------------------------
r530 | gaser | 2013-11-25 16:57:29 +0100 (Mon, 25 Nov 2013) | 4 lines

Changed paths:

Updated binaries for CAT.maci.

------------------------------------------------------------------------
r529 | gaser | 2013-11-25 16:56:48 +0100 (Mon, 25 Nov 2013) | 23 lines

Changed paths:
D       CAT.glnx86/CAT_DeformSurf_ui
D       CAT.glnx86/CAT_Obj2Neurolens
D       CAT.glnx86/CAT_ReconSurf
D       CAT.glnx86/CAT_ResampleFS_ui
RM      CAT.maci64/CAT_3dVol2Surf
RM      CAT.maci64/CAT_AddValuesToSurf
RM      CAT.maci64/CAT_BlurSurfHK
RM      CAT.maci64/CAT_DeformSurf
RM      CAT.maci64/CAT_DumpCurv
RM      CAT.maci64/CAT_DumpGI
RM      CAT.maci64/CAT_FixTopology
RM      CAT.maci64/CAT_FractalDimension
RM      CAT.maci64/CAT_Isometize
RM      CAT.maci64/CAT_LBConformalMap
RM      CAT.maci64/CAT_ResampleSphericalSurf
RM      CAT.maci64/CAT_ResampleSurf
RM      CAT.maci64/CAT_SeparatePolygon
RM      CAT.maci64/CAT_Surf2Sphere
RM      CAT.maci64/CAT_WarpSurf

Updated binaries for CAT.maci.

------------------------------------------------------------------------
r528 | gaser | 2013-11-25 16:52:42 +0100 (Mon, 25 Nov 2013) | 4 lines

Changed paths:

Updated binaries for CAT.maci.

------------------------------------------------------------------------
r527 | gaser | 2013-11-25 16:35:00 +0100 (Mon, 25 Nov 2013) | 19 lines

Changed paths:
M       CAT.maci64/CAT_3dVol2Surf
M       CAT.maci64/CAT_AddValuesToSurf
M       CAT.maci64/CAT_BlurSurfHK
M       CAT.maci64/CAT_DeformSurf
M       CAT.maci64/CAT_DumpCurv
M       CAT.maci64/CAT_DumpGI
M       CAT.maci64/CAT_FixTopology
M       CAT.maci64/CAT_FractalDimension
M       CAT.maci64/CAT_Isometize
M       CAT.maci64/CAT_LBConformalMap
M       CAT.maci64/CAT_ResampleSphericalSurf
M       CAT.maci64/CAT_ResampleSurf
M       CAT.maci64/CAT_SeparatePolygon
M       CAT.maci64/CAT_Surf2Sphere
M       CAT.maci64/CAT_WarpSurf

Updated binaries for CAT.maci.

------------------------------------------------------------------------
r526 | gaser | 2013-11-25 11:50:55 +0100 (Mon, 25 Nov 2013) | 53 lines

Changed paths:
 M      CAT.glnx86/CAT_3dVol2Surf
 M      CAT.glnx86/CAT_AddValuesToSurf
 M      CAT.glnx86/CAT_BlurSurfHK
 M      CAT.glnx86/CAT_DeformSurf
MM      CAT.glnx86/CAT_DeformSurf_ui
 M      CAT.glnx86/CAT_DumpCurv
 M      CAT.glnx86/CAT_DumpGI
 M      CAT.glnx86/CAT_FixTopology
 M      CAT.glnx86/CAT_FractalDimension
 M      CAT.glnx86/CAT_Isometize
 M      CAT.glnx86/CAT_LBConformalMap
 M      CAT.glnx86/CAT_Obj2Neurolens
MM      CAT.glnx86/CAT_ReconSurf
MM      CAT.glnx86/CAT_ResampleFS_ui
 M      CAT.glnx86/CAT_ResampleSphericalSurf
 M      CAT.glnx86/CAT_ResampleSurf
 M      CAT.glnx86/CAT_SeparatePolygon
 M      CAT.glnx86/CAT_Surf2Sphere
 M      CAT.glnx86/CAT_WarpSurf
MM      CAT.maci64/CAT_3dVol2Surf
 M      CAT.maci64/CAT_AddValuesToSurf
 M      CAT.maci64/CAT_BlurSurfHK
 M      CAT.maci64/CAT_DumpCurv
 M      CAT.maci64/CAT_DumpGI
MM      CAT.maci64/CAT_FractalDimension
MM      CAT.maci64/CAT_Isometize
 M      CAT.maci64/CAT_LBConformalMap
 M      CAT.maci64/CAT_ResampleSphericalSurf
 M      CAT.maci64/CAT_ResampleSurf
MM      CAT.maci64/CAT_WarpSurf
MM      CAT.win32/CAT_3dVol2Surf.exe
MM      CAT.win32/CAT_AddValuesToSurf.exe
MM      CAT.win32/CAT_BlurSurfHK.exe
MM      CAT.win32/CAT_DeformSurf.exe
MM      CAT.win32/CAT_DumpCurv.exe
MM      CAT.win32/CAT_DumpGI.exe
MM      CAT.win32/CAT_FixTopology.exe
MM      CAT.win32/CAT_FractalDimension.exe
MM      CAT.win32/CAT_Isometize.exe
MM      CAT.win32/CAT_LBConformalMap.exe
MM      CAT.win32/CAT_ResampleSphericalSurf.exe
MM      CAT.win32/CAT_ResampleSurf.exe
MM      CAT.win32/CAT_SeparatePolygon.exe
MM      CAT.win32/CAT_Surf2Sphere.exe
MM      CAT.win32/CAT_WarpSurf.exe
MM      fsaverage/lh.smoothwm
 M      fsaverage/lh.sphere
MM      fsaverage/rh.smoothwm
 M      fsaverage/rh.sphere

Updated binaries for CAT.

------------------------------------------------------------------------
r525 | gaser | 2013-11-22 16:28:59 +0100 (Fri, 22 Nov 2013) | 10 lines

Changed paths:

(1) Corrected output for texture files (e.g. thickness) in vbm_io_FreeSurfer.m.
(2) Thickness (ROI) output is only provided if extopts.surface is set in
    cg_vbm_defaults.m.
(3) Added executables for CAT.
(4) Changed system calls in vbm_surf_createCS.
(5) Added and changed surface filenames according to freesurfer notation.


------------------------------------------------------------------------
r524 | gaser | 2013-11-22 16:27:45 +0100 (Fri, 22 Nov 2013) | 81 lines

Changed paths:
D       CAT
D       CAT/CAT_DeformSurf
D       CAT/CAT_DeformSurf_ui
D       CAT/CAT_FixTopology
D       CAT/CAT_SeparateCluster
D       CAT/CAT_SeparatePolygon
D       CAT/CAT_Surf2Sphere
A       CAT.glnx86
A       CAT.glnx86/CAT_3dVol2Surf
A       CAT.glnx86/CAT_AddValuesToSurf
A       CAT.glnx86/CAT_BlurSurfHK
A       CAT.glnx86/CAT_DeformSurf
A       CAT.glnx86/CAT_DeformSurf_ui
A       CAT.glnx86/CAT_DumpCurv
A       CAT.glnx86/CAT_DumpGI
A       CAT.glnx86/CAT_FixTopology
A       CAT.glnx86/CAT_FractalDimension
A       CAT.glnx86/CAT_Isometize
A       CAT.glnx86/CAT_LBConformalMap
A       CAT.glnx86/CAT_Obj2Neurolens
A       CAT.glnx86/CAT_ReconSurf
A       CAT.glnx86/CAT_ResampleFS_ui
A       CAT.glnx86/CAT_ResampleSphericalSurf
A       CAT.glnx86/CAT_ResampleSurf
A       CAT.glnx86/CAT_SeparatePolygon
A       CAT.glnx86/CAT_Surf2Sphere
A       CAT.glnx86/CAT_WarpSurf
A  +    CAT.maci64
A       CAT.maci64/CAT_3dVol2Surf
A       CAT.maci64/CAT_AddValuesToSurf
A       CAT.maci64/CAT_BlurSurfHK
M  +    CAT.maci64/CAT_DeformSurf
D  +    CAT.maci64/CAT_DeformSurf_ui
A       CAT.maci64/CAT_DumpCurv
A       CAT.maci64/CAT_DumpGI
M  +    CAT.maci64/CAT_FixTopology
A       CAT.maci64/CAT_FractalDimension
A       CAT.maci64/CAT_Isometize
A       CAT.maci64/CAT_LBConformalMap
A       CAT.maci64/CAT_ResampleSphericalSurf
A       CAT.maci64/CAT_ResampleSurf
D  +    CAT.maci64/CAT_SeparateCluster
M  +    CAT.maci64/CAT_SeparatePolygon
M  +    CAT.maci64/CAT_Surf2Sphere
A       CAT.maci64/CAT_WarpSurf
A       CAT.win32
A       CAT.win32/CAT_3dVol2Surf.exe
A       CAT.win32/CAT_AddValuesToSurf.exe
A       CAT.win32/CAT_BlurSurfHK.exe
A       CAT.win32/CAT_DeformSurf.exe
A       CAT.win32/CAT_DumpCurv.exe
A       CAT.win32/CAT_DumpGI.exe
A       CAT.win32/CAT_FixTopology.exe
A       CAT.win32/CAT_FractalDimension.exe
A       CAT.win32/CAT_Isometize.exe
A       CAT.win32/CAT_LBConformalMap.exe
A       CAT.win32/CAT_ResampleSphericalSurf.exe
A       CAT.win32/CAT_ResampleSurf.exe
A       CAT.win32/CAT_SeparatePolygon.exe
A       CAT.win32/CAT_Surf2Sphere.exe
A       CAT.win32/CAT_WarpSurf.exe
M       Makefile.vbm
M       cg_vbm_defaults.m
M       cg_vbm_write.m
A       fsaverage
A       fsaverage/lh.smoothwm
A       fsaverage/lh.sphere
A       fsaverage/rh.smoothwm
A       fsaverage/rh.sphere
M       vbm_io_FreeSurfer.m
M       vbm_surf_createCS.m

(1) Corrected output for texture files (e.g. thickness) in vbm_io_FreeSurfer.m.
(2) Thickness (ROI) output is only provided if extopts.surface is set in
    cg_vbm_defaults.m.
(3) Added executables for CAT.
(4) Changed system calls in vbm_surf_createCS.
(5) Added and changed surface filenames according to freesurfer notation.


------------------------------------------------------------------------
r523 | dahnke | 2013-11-20 12:53:33 +0100 (Wed, 20 Nov 2013) | 24 lines

Changed paths:
A       CAT
A       CAT/CAT_DeformSurf
A       CAT/CAT_DeformSurf_ui
A       CAT/CAT_FixTopology
A       CAT/CAT_SeparateCluster
A       CAT/CAT_SeparatePolygon
A       CAT/CAT_Surf2Sphere
M       cg_vbm_batch.m
M       cg_vbm_defaults.m
M       cg_vbm_write.m
A       vbm_io_FreeSurfer.m
M       vbm_io_writenii.m
A       vbm_surf_createCS.m
M       vbm_tst_pre.m
M       vbm_vol_resize.m

(1)  Corrected jacobian output.
(2)  Update thickness estimation and move it to vbm_surf_createCS.
(3)  Add surface reconstruction and thickness estimation (vbm_surf_createCS).
     This function include the topology correction and shape refinements for
     left and right hemispheres. The option "vbm.extopts.surface" in the
     cg_vbm_defaults-file controls surface estimation.

------------------------------------------------------------------------
r522 | gaser | 2013-11-19 15:13:36 +0100 (Tue, 19 Nov 2013) | 12 lines

Changed paths:
M       cg_vbm_batch.m
MM      templates_1.50mm/aal.txt
MM      templates_1.50mm/anatomy.txt
 M      templates_1.50mm/mori.csv
 M      templates_1.50mm/mori.nii
MM      templates_1.50mm/mori.txt
M       vbm_io_writenii.m

Some small changes in cg_vbm_batch.m and changed names for affine files
in vbmi_io_writenii.m

------------------------------------------------------------------------
r521 | gaser | 2013-11-19 13:16:08 +0100 (Tue, 19 Nov 2013) | 17 lines

Changed paths:
M       cg_cfg_realign.m
M       cg_vbm_defaults.m
M       cg_vbm_tools.m
M       cg_vbm_write.m
MM      spm_def2det.c
 M      spm_def2det.mexa64
 M      spm_def2det.mexglx
 M      spm_def2det.mexmaci
 M      spm_def2det.mexmaci64
 M      spm_def2det.mexw32
 M      spm_def2det.mexw64
M       vbm12.man

Removed some bugs in cg_vbm_write.m and removed flags that are not needed
anymore in cg_vbm_defaults.m.

------------------------------------------------------------------------
r520 | dahnke | 2013-11-19 08:46:54 +0100 (Tue, 19 Nov 2013) | 38 lines

Changed paths:
M       CHANGES.txt
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       ds.m
D       images
M       tbx_cfg_vbm.m
M       templates_1.50mm/aal.csv
M       templates_1.50mm/aal.nii
A       templates_1.50mm/aal.txt
M       templates_1.50mm/anatomy.csv
M       templates_1.50mm/anatomy.nii
A       templates_1.50mm/anatomy.txt
M       templates_1.50mm/hammers.csv
M       templates_1.50mm/hammers.nii
A       templates_1.50mm/hammers.txt
M       templates_1.50mm/ibsr.csv
M       templates_1.50mm/ibsr.nii
A       templates_1.50mm/ibsr.txt
D       templates_1.50mm/jhu.nii
A       templates_1.50mm/mori.csv
A       templates_1.50mm/mori.nii
A       templates_1.50mm/mori.txt
M       vbm_io_writenii.m
M       vbm_tst_pre.m
M       vbm_vol_atlas.m
M       vbm_vol_localstat.c
M       vbm_vol_localstat.mexmaci64

(1)  Update VBM Menu.
(2)  Removed thickness maps output.
(3)  Update vbm_vol_atlas (skript for atlas creation), with merging of different
     ROIs and final side alignment with left (odd) and right (even) labels.
(4)  Update all atlas maps. Add a text-file with most important atlas information
     and a csv-file for ROI-IDs, ROI-names, and ROI-appresservation.
(5)  Create subfunctions for ROI mapping and value estimation.
(6)  Correct "projection" error in vbm_io_writenii for images without mask.

------------------------------------------------------------------------
r519 | gaser | 2013-11-13 13:35:38 +0100 (Wed, 13 Nov 2013) | 6 lines

Changed paths:
M       tbx_cfg_vbm.m
M       vbm12.man

Corrected wrong datatype for gcut+ strnegth in tbx_cfg_vbm.m

------------------------------------------------------------------------
r518 | dahnke | 2013-11-07 13:11:56 +0100 (Thu, 07 Nov 2013) | 44 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_defs.m
M       cg_vbm_write.m
M       compile.m
A       spm_def2det.c
A       spm_def2det.mexa64
A       spm_def2det.mexglx
A       spm_def2det.mexmaci
A       spm_def2det.mexmaci64
A       spm_def2det.mexw32
A       spm_def2det.mexw64
M       tbx_cfg_vbm.m
A       templates_1.50mm/aal.csv
M       templates_1.50mm/aal.nii
A       templates_1.50mm/anatomy.csv
A       templates_1.50mm/anatomy.nii
A       templates_1.50mm/hammers.csv
A       templates_1.50mm/hammers.nii
A       templates_1.50mm/ibsr.csv
A       templates_1.50mm/ibsr.nii
A       templates_1.50mm/jhu.nii
M       vbm_io_csv.m
M       vbm_io_writenii.m
A       vbm_vol_atlas.m
A       vbm_vol_eidist.c
D       vbm_vol_eidist.cpp
M       vbm_vol_eidist.mexmaci64
M       vbm_vol_localstat.c
M       vbm_vol_localstat.mexmaci64

(1)  Add atlas maps for alpha tests.
     1) IBSR:     label map of 18 subjects (major & subcortical ROIs)
     2) Hammers:  label map of 20 subjects (major, neocortex & subcortical ROIs)
     3) JHU:      label map of  1 subject with complete labeling
     4) AAL:      label map of  1 subject with complete labeling (Collins)
     5) Anatomy:  label map of 10 persons with incomplete labeling
(2)  Add spm_def2det temporary for cg_vbm_defs, because it was removed in VBM12.
(3)  Atlas generation scripts.
(4)  Replace vbm_vol_eidist.cpp by vbm_vol_eidist.c.
(5)  Update vbm_vol_localstat by median-like filteroption.
(6)  Update vbm_io_writenii for masking and label mapping.
(7)  Update ROI options in cg_vbm_defaults.

------------------------------------------------------------------------
r517 | gaser | 2013-11-06 12:43:55 +0100 (Wed, 06 Nov 2013) | 10 lines

Changed paths:
M       cg_cfg_realign.m
M       cg_vbm_tools.m
M       tbx_cfg_vbm.m
 M      templates_1.50mm/aal.nii
 M      templates_1.50mm/brodmann.nii

Changed strtype-parameters from 'e' to either 'r' (real value) or 'n' (integer)
according to new spm12b update r5731.

------------------------------------------------------------------------
r516 | gaser | 2013-11-01 08:12:22 +0100 (Fri, 01 Nov 2013) | 5 lines

Changed paths:
M       tbx_cfg_vbm.m

Removed some typos.

------------------------------------------------------------------------
r515 | dahnke | 2013-10-30 15:47:16 +0100 (Wed, 30 Oct 2013) | 8 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       vbm_io_writenii.m

(1)  Add ROI export for normalized space.


------------------------------------------------------------------------
r514 | dahnke | 2013-10-28 18:22:52 +0100 (Mon, 28 Oct 2013) | 27 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       tbx_cfg_vbm.m
A       templates_1.50mm/aal.nii
A       templates_1.50mm/brodmann.nii
M       vbm_io_writenii.m
M       vbm_tst_pre.m
M       vbm_tst_t1qa.m
M       vbm_vol_eidist.cpp
M       vbm_vol_eidist.mexmaci64

(1)  Add masked export option for vbm_io_writenii for a correct mapping of local
     defined maps like the cortical thickness map th1.
(2)  Add label export option for vbm_io_writenii for a correct mapping of atlas
     maps l#.
(3)  Add 2 atlas maps (aal, brodmann) to template_1.50mm directory and a simple
     mapping routine without further refinements. (The *.csv Files of both are
     still missing, but for a first test its ok).
(4)  Simplify m* output, where also the locally intensity corrected image of the
     LAS part is saved under this name.
(5)  Correct segmentation input for the gcut+ path. Previous, old SPM maps lead
     to problems with the skull-stripping.
(6)  Add a function that estimates the volumes, intensity and thickness values
     for each ROI of the atlas maps in subject space and write this data to a
     csv-file per atlas and to the vbm_*.xml.

------------------------------------------------------------------------
r513 | dahnke | 2013-10-26 18:35:40 +0200 (Sat, 26 Oct 2013) | 49 lines

Changed paths:
M       CHANGES.txt
M       cg_vbm_batch.sh
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       tbx_cfg_vbm.m
M       vbm_io_colormaps.m
A       vbm_io_img2nii.m
M       vbm_io_updateStruct.m
M       vbm_io_writenii.m
M       vbm_io_xml.m
A       vbm_plot_boxplot.m
M       vbm_tst_pre.m
A       vbm_tst_qa_groups.m
A       vbm_tst_qa_groups_test.m
M       vbm_tst_t1qa.m
M       vbm_vol_partvol.m
M       vbm_vol_sanlm.m

(1)  Updates of cg_vbm_batch.sh:
     - add symbolic link detection in subfunction check_files
     - add checks for subfunction get_no_of_cpus to limit the number of jobs
       by the number of processors
     - add options:
       -n   nice level
       -s   shell command
       -f   file with files to process
            got a system error 127 for a large number (>1000) of files for
            direct input
       -np  set number of free processors/cores, to have always on free
            processor/core (-np 1)
(2)  Update vbm_io_xml write with orderfields function.
(3)  Add verbose option for vbm_io_xml to get feedback for reading large number
     of files (>1000).
(4)  Add prefix-variable for vbm_pre_sanlm.
(5)  Further QMs in vbm_tst_t1qa.
(6)  Replace struct2array in vbm_vol_partvol and cg_vbm_write, because the
     function was remove in newer MATLAB versions.
(7)  Add parameter to control gcut+ Skull-Stripping.
(8)  Add some comments.
(9)  Add vbm_tst_qa_groups[_test] for QA analysis.
(10) Add vbm_io_img2nii to convert analyse files to nifti.
(11) Correct error in vbm_io_colormaps (number of colors).
(12) Add skull-stripping strength variable that controls, different parameter
     like intensity-thresholds, region-growing-parameter, closing and smoothness
     parameter. The parameter should be between 0 and 1, with 0 for wider and
     smoother masks and 1 for harder results (default 0.5).


------------------------------------------------------------------------
r512 | gaser | 2013-10-15 10:02:34 +0200 (Tue, 15 Oct 2013) | 7 lines

Changed paths:
M       AmapMex.c
M       AmapMex.mexmaci64
M       KmeansMex.c

Replaced free in AmapMex.c and KmeanMex.c with mxFree.

------------------------------------------------------------------------
r511 | gaser | 2013-10-15 09:55:38 +0200 (Tue, 15 Oct 2013) | 55 lines

Changed paths:
 M      vbm_vol_pbtp.mexa64
 M      vbm_vol_laplace3.mexw64
 M      vbm_vol_gradient3.mexglx
 M      vbm_vol_median3.mexglx
 M      vbm_vol_eidist.mexa64
 M      vbm_vol_eikonal3.mexw32
 M      vbm_vol_interp3f.mexglx
 M      vbm_vol_median3c.mexw32
 M      vbm_vol_simgrow.mexw32
 M      vbm_vol_downcut.mexw64
 M      vbm_vol_laplace3.mexglx
 M      vbm_vol_pbtp.mexw32
 M      vbm_vol_laplace3R.mexw64
 M      vbm_vol_eidist.mexw32
 M      vbm_vol_localstat.mexw64
 M      vbm_vol_median3.mexa64
 M      vbm_vol_gradient3.mexa64
 M      vbm_vol_downcut.mexglx
 M      vbm_vol_interp3f.mexa64
 M      vbm_vol_laplace3R.mexglx
M       AmapMex.c
 M      vbm_vol_laplace3.mexa64
 M      vbm_vol_localstat.mexglx
 M      vbm_vol_eikonal3.mexw64
M       AmapMex.mexmaci64
 M      vbm_vol_median3.mexw32
 M      vbm_vol_gradient3.mexw32
 M      vbm_vol_median3c.mexw64
 M      vbm_vol_interp3f.mexw32
 M      vbm_vol_simgrow.mexw64
 M      vbm_vol_downcut.mexa64
 M      vbm_vol_pbtp.mexw64
 M      vbm_vol_laplace3.mexw32
 M      vbm_vol_eikonal3.mexglx
 M      vbm_vol_laplace3R.mexa64
 M      vbm_vol_eidist.mexw64
 M      vbm_vol_median3c.mexglx
 M      vbm_vol_localstat.mexa64
 M      vbm_vol_simgrow.mexglx
 M      vbm_vol_downcut.mexw32
 M      vbm_vol_pbtp.mexglx
 M      vbm_vol_eidist.mexglx
M       KmeansMex.c
 M      vbm_vol_laplace3R.mexw32
 M      vbm_vol_eikonal3.mexa64
 M      vbm_vol_gradient3.mexw64
 M      vbm_vol_median3.mexw64
 M      vbm_vol_localstat.mexw32
 M      vbm_vol_interp3f.mexw64
 M      vbm_vol_median3c.mexa64
 M      vbm_vol_simgrow.mexa64

Replaced malloc in AmapMex.c with mxMalloc.

------------------------------------------------------------------------
r510 | gaser | 2013-10-14 18:33:37 +0200 (Mon, 14 Oct 2013) | 7 lines

Changed paths:
M       Kmeans.c
M       vollib.c
M       vbm12.man

Replaced fprintf with printf to allow output for windows platforms.

------------------------------------------------------------------------
r509 | gaser | 2013-10-14 16:35:33 +0200 (Mon, 14 Oct 2013) | 52 lines

Changed paths:
A       vbm_vol_pbtp.mexa64
A       vbm_vol_laplace3.mexw64
A       vbm_vol_median3.mexglx
A       vbm_vol_gradient3.mexglx
A       vbm_vol_eidist.mexa64
A       vbm_vol_eikonal3.mexw32
A       vbm_vol_interp3f.mexglx
A       vbm_vol_median3c.mexw32
A       vbm_vol_simgrow.mexw32
A       vbm_vol_downcut.mexw64
A       vbm_vol_laplace3.mexglx
A       vbm_vol_pbtp.mexw32
A       vbm_vol_laplace3R.mexw64
A       vbm_vol_eidist.mexw32
A       vbm_vol_localstat.mexw64
A       vbm_vol_gradient3.mexa64
A       vbm_vol_median3.mexa64
A       vbm_vol_downcut.mexglx
A       vbm_vol_interp3f.mexa64
A       vbm_vol_laplace3R.mexglx
A       vbm_vol_laplace3.mexa64
A       vbm_vol_localstat.mexglx
A       vbm_vol_eikonal3.mexw64
A       vbm_vol_gradient3.mexw32
A       vbm_vol_median3.mexw32
A       vbm_vol_median3c.mexw64
A       vbm_vol_interp3f.mexw32
A       vbm_vol_simgrow.mexw64
A       vbm_vol_downcut.mexa64
A       vbm_vol_pbtp.mexw64
A       vbm_vol_laplace3.mexw32
A       vbm_vol_eikonal3.mexglx
A       vbm_vol_laplace3R.mexa64
A       vbm_vol_eidist.mexw64
A       vbm_vol_median3c.mexglx
A       vbm_vol_localstat.mexa64
A       vbm_vol_simgrow.mexglx
A       vbm_vol_downcut.mexw32
A       vbm_vol_pbtp.mexglx
A       vbm_vol_eidist.mexglx
A       vbm_vol_laplace3R.mexw32
A       vbm_vol_eikonal3.mexa64
A       vbm_vol_gradient3.mexw64
A       vbm_vol_median3.mexw64
A       vbm_vol_localstat.mexw32
A       vbm_vol_interp3f.mexw64
A       vbm_vol_median3c.mexa64
A       vbm_vol_simgrow.mexa64

Added missing mex-files.

------------------------------------------------------------------------
r508 | gaser | 2013-10-14 16:33:59 +0200 (Mon, 14 Oct 2013) | 24 lines

Changed paths:
M       sanlmMex.mexw32
M       vbm_vol_eidist.mexmaci64
M       vbm_vol_pbtp.cpp
M       AmapMex.mexw32
M       compile.m
M       vbm_vol_simgrow.c
M       vbm_vol_simgrow.mexmaci64
M       sanlmMex.mexw64
M       vbdist.mexw32
M       sanlmMex.mexglx
M       AmapMex.mexw64
M       vbm_vol_pbtp.mexmaci64
M       vbm_vol_localstat.c
M       vbm12.man
M       vbm_vol_localstat.mexmaci64
M       vbdist.mexw64
M       vbm_vol_eidist.cpp
M       vbm_vol_median3c.mexmaci64

(1) Added missing files to compile.m.
(2) Modified c/c++ code to allow compiling for linux/windows.
(3) Re-compiling for all platforms.

------------------------------------------------------------------------
r507 | gaser | 2013-09-30 12:54:54 +0200 (Mon, 30 Sep 2013) | 8 lines

Changed paths:
M       cg_vbm_run.m
M       cg_vbm_write.m

(1) Removed unused paramter Fn from cg_vbm_run.m.
(2) Again some cleaning of filenames in cg_vbm_write.m and removing some minor
    typos and bugs.

------------------------------------------------------------------------
r506 | gaser | 2013-09-25 16:42:06 +0200 (Wed, 25 Sep 2013) | 7 lines

Changed paths:
M       cg_vbm_run.m
M       cg_vbm_write.m

Many changes to cg_vbm_write and cg_vbm_run to clean up the mess with the
filenames.

------------------------------------------------------------------------
r505 | gaser | 2013-09-25 13:04:05 +0200 (Wed, 25 Sep 2013) | 19 lines

Changed paths:
M       vbm_vol_median3.mexmaci64
M       vbm_vol_gradient3.mexmaci64
M       AmapMex.mexmaci64
M       vbm_vol_downcut.mexmaci64
M       vbm_vol_eikonal3.mexmaci64
M       sanlmMex.mexmaci64
M       vbm_vol_laplace3R.mexmaci64
M       vbdist.mexmaci64
M       sanlmMex_noopenmp.mexmaci64
M       vbm_vol_laplace3.mexmaci64
M       cg_vbm_write.m
M       vbm_vol_interp3f.mexmaci64

(1) Removed bug in cg_vbm_writewhere no img-files could be used if
    SANLM-filter was used and nii-extension was forced.
(2) Re-compiling for macosx.


------------------------------------------------------------------------
r504 | gaser | 2013-09-24 17:13:20 +0200 (Tue, 24 Sep 2013) | 8 lines

Changed paths:
M       compile.m
M       sanlmMex.mexa64

(1) Modified c/c++ code to allow compiling for linux/windows.
(2) Re-compiling for linux/windows.
(3) Changed compile.m to consider new paths for libgomp.a.

------------------------------------------------------------------------
r503 | gaser | 2013-09-24 17:02:13 +0200 (Tue, 24 Sep 2013) | 21 lines

Changed paths:
M       vbdist.mexglx
M       vbm_vol_gradient3.c
M       AmapMex.mexa64
M       vbdist.mexa64
M       AmapMex.mexw32
M       vbdist.mexw32
M       vbm_vol_downcut.c
M       sanlmMex_noopenmp.mexglx
M       vbm_vol_eikonal3.c
M       sanlmMex.mexglx
M       vbm_vol_laplace3R.c
M       vbm_vol_laplace3.c
M       vbm_vol_interp3f.cpp
M       sanlmMex_noopenmp.mexa64
M       sanlmMex.mexa64
M       AmapMex.mexglx

(1) Modified c/c++ code to allow compiling for linux/windows.
(2) Re-compiling for linux/windows.

------------------------------------------------------------------------
r502 | gaser | 2013-09-23 16:41:10 +0200 (Mon, 23 Sep 2013) | 5 lines

Changed paths:
M       cg_vbm_run.m

Option to write already estimated segmentations can now deal with additional denoising in cg_vbm_run.m.

------------------------------------------------------------------------
r501 | gaser | 2013-09-23 14:56:37 +0200 (Mon, 23 Sep 2013) | 7 lines

Changed paths:
M       vbm_vol_resize.m
M       cg_vbm_write.m

(1) Force to write single typed data in vbm_vol_resize.m for 'dereducebrain'.
(2) Cleaned up some variables to save memory in cg_vbm_write.m.

------------------------------------------------------------------------
r500 | gaser | 2013-09-23 13:04:00 +0200 (Mon, 23 Sep 2013) | 5 lines

Changed paths:

(1) Force to write single typed data in vbm_vol_resize.m for 'dereducebrain'.
(2) Cleaned up some variables to save memory in cg_vbm_write.m.

------------------------------------------------------------------------
r499 | dahnke | 2013-09-20 13:01:10 +0200 (Fri, 20 Sep 2013) | 7 lines

Changed paths:
M       cg_vbm_run.m
M       cg_vbm_write.m
M       compile.m



------------------------------------------------------------------------
r498 | gaser | 2013-09-20 09:41:00 +0200 (Fri, 20 Sep 2013) | 10 lines

Changed paths:
M       Makefile.vbm
M       cg_vbm_run.m
M       cg_vbm_write.m

(1) Variable Fn in cg_vbm_run.m was not available if "write only" option
    was used.
(2) Dartel is deselected if nor normalized images need to be saved in
    cg_vbm_write.m

------------------------------------------------------------------------
r497 | dahnke | 2013-09-18 13:06:11 +0200 (Wed, 18 Sep 2013) | 20 lines

Changed paths:
 M      templates_1.50mm
A       vbm_check.m
A       vbm_db.m
A       vbm_db_batch.m
 M      vbm_io_cgw2seg.m
MM      vbm_io_csv.m
A       vbm_io_mysql.m
 M      vbm_io_remat.m
MM      vbm_io_seg2cgw.m
 M      vbm_tst_SRS.m
MM      vbm_tst_pre.m
 M      vbm_tst_staple_multilabels.m
A       vbm_tst_t1qa.m
MM      vbm_vol_average.m
MM      vbm_vol_sanlm.m

(1) Add VBM database development files (vbm_db_batch, vbm_db, vbm_io_mysql).
(2) Add QM estimation (vbm_tst_t1qa).

------------------------------------------------------------------------
r496 | dahnke | 2013-09-16 17:54:41 +0200 (Mon, 16 Sep 2013) | 24 lines

Changed paths:
M       cg_vbm_write.m
A       vbm_io_cgw2seg.m
A       vbm_io_csv.m
A       vbm_io_remat.m
A       vbm_io_seg2cgw.m
A       vbm_tst_SRS.m
M       vbm_tst_calc_bias.m
M       vbm_tst_calc_kappa.m
A       vbm_tst_pre.m
A       vbm_tst_staple_multilabels.m
A       vbm_vol_average.m
M       vbm_vol_laplace3R.c
M       vbm_vol_laplace3R.mexmaci64
A       vbm_vol_sanlm.m

(1) Add scan-rescan test skripts (vbm_tst_SRS).
(2) Add function to convert p0 segment maps into c1, c2, c3 probability/PVE maps (vbm_io_seg2cgw).
(3) Add function to convert c1, c2, c3 probability/PVE maps into p0 segment maps (vbm_io_cgw2seg).
(4) Add csv-import/export function (vbm_io_csv).
(5) Add average function for images with similar properties to create a median-, mean-, and std image (vbm_vol_average).
(6) Add STAPLE segmentation (vbm_tst_staple_multilabels).
(7) Update quality measures.

------------------------------------------------------------------------
r495 | gaser | 2013-07-09 13:05:57 +0200 (Tue, 09 Jul 2013) | 14 lines

Changed paths:
 M      vbm_tst_calc_bias.m
 M      templates_1.50mm/Template_1_IXI550_MNI152.nii
 M      templates_1.50mm/Template_2_IXI550_MNI152.nii
 M      templates_1.50mm/Template_3_IXI550_MNI152.nii
 M      templates_1.50mm/Template_4_IXI550_MNI152.nii
 M      templates_1.50mm/Template_5_IXI550_MNI152.nii
 M      templates_1.50mm/Template_6_IXI550_MNI152.nii
 M      templates_1.50mm/TPM.nii
M       cg_vbm_run.m
 M      vbm_tst_calc_kappa.m

Corrected errors in cg_vbm_run.m when already estimated segmentations were used.

------------------------------------------------------------------------
r494 | gaser | 2013-07-09 12:42:46 +0200 (Tue, 09 Jul 2013) | 5 lines

Changed paths:
M       cg_vbm_run.m

Cleaned code in cg_vbm_run.m and removed parts that were not necessary anymore.

------------------------------------------------------------------------
r493 | dahnke | 2013-06-27 10:12:27 +0200 (Thu, 27 Jun 2013) | 20 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       tbx_cfg_vbm.m
M       vbm_io_xml.m
M       vbm_stat_marks.m
A       vbm_tst_calc_bias.m
A       vbm_tst_calc_kappa.m
M       vbm_vol_partvol.m
M       vbm_vol_pbt.m
M       vbm_vol_resize.m
M       vbm_vol_t1qacalc.m

(1) Multiple file input for vbm_io_xml.
(2) Corrected ventricle closing problems for large ventricle (OASIS21,4397) and
    small updates of the skull-stripping
(3) Updates of vbm_vol_resize for better support of NaN's in images.
(4) Add kappa and bias estimation test skripts.


------------------------------------------------------------------------
r492 | dahnke | 2013-05-30 16:51:58 +0200 (Thu, 30 May 2013) | 24 lines

Changed paths:
D       Template_1_IXI550_MNI152.nii
D       Template_2_IXI550_MNI152.nii
D       Template_3_IXI550_MNI152.nii
D       Template_4_IXI550_MNI152.nii
D       Template_5_IXI550_MNI152.nii
D       Template_6_IXI550_MNI152.nii
M       cg_vbm_defaults.m
M       cg_vbm_run.m
M       cg_vbm_write.m
A       templates_1.50mm/TPM.nii
A       templates_1.50mm/Template_1_IXI550_MNI152.nii
A       templates_1.50mm/Template_2_IXI550_MNI152.nii
A       templates_1.50mm/Template_3_IXI550_MNI152.nii
A       templates_1.50mm/Template_4_IXI550_MNI152.nii
A       templates_1.50mm/Template_5_IXI550_MNI152.nii
A       templates_1.50mm/Template_6_IXI550_MNI152.nii
M       vbm_stat_marks.m
M       vbm_vol_partvol.m
M       vbm_vol_t1qacalc.m

(1) Moved VBM IXI Dartel template to template directory.
(2) Added VBM 7 class segmentation image TPM.nii to template directory.

------------------------------------------------------------------------
r491 | dahnke | 2013-05-28 16:48:26 +0200 (Tue, 28 May 2013) | 22 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_run.m
M       cg_vbm_write.m
M       tbx_cfg_vbm.m
M       vbm_io_updateStruct.m
M       vbm_stat_marks.m
M       vbm_vol_partvol.m
M       vbm_vol_resize.m
M       vbm_vol_t1qacalc.m

(1) Move the noise correction before the SPM preprocessing.
    Rename *_seg8.mat to vbm12mat_*.mat to have blocks of image/file-types.
(2) Move the partition behind the local adaptive segmentation, because it can
    profit from the normalization in all regions and because the local adaptive
    segmentation only requires the segmentation of the subcortical structures.
    The partitioning still requires some work and of course more test.
(3) Thickness calculation for both sides.
(4) Reduced the number of quality measures (switch-off the new and untested
    measures) for speed-up. Reduced variables to save memory.
(5) Removed unnecessary variables to save memory.

------------------------------------------------------------------------
r490 | dahnke | 2013-05-24 10:02:52 +0200 (Fri, 24 May 2013) | 20 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_run.m
M       cg_vbm_write.m
M       vbm_vol_partvol.m

This is just a sub-step with experimental elements that I want to save before
I change the next things...
(1) To obtain a better inhomogeneity correction SPM-default Parameter were
    changed (biasfwhm=30, samp=2), with better results but higher calculation
    time. Strong improvements for highres (Magdeburg7T and HR075) and lowres
    images (NIH1394). This works better than the additional maximum based
    correction and I will remove/uncomment the maximum correction. :/
(2) The Partition work not bad, but it is now very slow (>1 minute) and I have
    optimize many substeps (mostly by resizing to lower resolutions).
(3) Correction of the tissue peak estimation for the global intensity
    normalization for images with WM lessions (OASIS0031) that lead to error in
    the skull-stripping.
(4) Skull-Stripping of this version is still to aggressive.

------------------------------------------------------------------------
r489 | gaser | 2013-05-22 10:20:57 +0200 (Wed, 22 May 2013) | 8 lines

Changed paths:
M       cg_vbm_run.m
M       cg_vbm_batch.sh
M       vbm12.man

(1) Added missing stime variable in cg_vbm_run.
(2) Log-file for cg_vbm_batch.sh os now saved as default in current folder.

------------------------------------------------------------------------
r488 | dahnke | 2013-05-19 16:11:49 +0200 (Sun, 19 May 2013) | 17 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       vbm12.txt
 M      vbm_io_colormaps.m
M       vbm_io_cprintf.m
MM      vbm_stat_marks.m
M       vbm_vol_partvol.m

(1) Corrected resolution error in LAS skull-stripping.
(2) Rewrote parts of the partitioning.
(3) Corrected figure error, if spm_grafics was not the current figure.
(4) Prepare preprocessing for thickness phantom and test thickness measure.
(5) Update partitioning and add error messages for missing structures.



------------------------------------------------------------------------
r487 | dahnke | 2013-05-15 11:20:44 +0200 (Wed, 15 May 2013) | 35 lines

Changed paths:
M       cg_vbm_run.m
M       cg_vbm_write.m
M       vbm_stat_marks.m
M       vbm_vol_partvol.m

(1) Moving of the partitioning routines before the skull-stripping, to use the
    atlas map for skull-stripping to allow regional different growing rates.
    Although, now only SPM standard normalization is used, I expect a similar
    accuracy, because the partitioning use the atlas mostly for initialization
    followed by a region growing. The partitioning still requires more work to
    get smoother segments without removing anatomical details.
(2) Maximum-based bias correction and intensity scaling for global and local
    segmentation.
(3) Less aggressive local adaption with a stronger relation to SPM classes.
(4) Correct an SPM label error, where intracranial BG was labeled as CSF that
    produce CSF mean intensities that were to close to the BG intensity and
    CSF was detected as low GM. Correct also the other "direction" where CGM
(5) The partitioning routine allows now a direct mapping of the basal ganglia
    for maximum-based bias correction and local adaptive segmentation.
(6) New skull-stripping routine in the LAS pipeline (alpha status) with a harder
    brain extraction to reduce meninges and blood vessels that needs to be a
    little bit smoother:

               DICE     FP    FN
      VBM12i:  0.9632   4437  83478
      VBM12:   0.9720  21337  46823

(7) Deactivated BVC for inverse contrast.
(8) Command window output updates:
    - Added colored output for the filename output.
    - Added computation times for preprocessing steps.
    - Added final output with total computation time and with short QA results.
    - Final reduction of Dartel command window output.

------------------------------------------------------------------------
r486 | gaser | 2013-05-07 10:53:11 +0200 (Tue, 07 May 2013) | 6 lines

Changed paths:
M       Makefile.vbm
M       cg_vbm_batch.m

Updated filenames in cg_vbm_batch.m and Makefile.vbm.

------------------------------------------------------------------------
r485 | dahnke | 2013-05-03 18:16:06 +0200 (Fri, 03 May 2013) | 26 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       vbm12.txt
A       vbm_io_colormaps.m
M       vbm_io_xml.m
A       vbm_stat_marks.m
M       vbm_vol_partvol.m
M       vbm_vol_t1qacalc.m

(1) Modality check to process PD and T2 images, with intensity inversion for
    standard preprocessing, if vbm.extopts.INV=1.
(2) Resolution check to avoid preprocessing of low resolution images.
(3) Added JVM error in vbm_io_xml, if JVM is inactive.
(4) VBM report:
    - Subject specific measures (global volume and thickness).
    - Color-coded marks for a faster overview.
    - Added subject report (vbm_*.ps) file.
    - Added changeable colormaps and colorbar.
    - Added image names.
    - Added vbm-colormaps.
    - Added more flexible output images (mix of different spaces), all images
      were cropped by the default boundary box.
(5) Updated MRF-filter setting, where vbm.extopts.mrf=1 will use the adaptive
    MRF-filter strength (default).

------------------------------------------------------------------------
r484 | gaser | 2013-04-29 16:10:33 +0200 (Mon, 29 Apr 2013) | 7 lines

Changed paths:
M       Makefile.vbm
M       cg_vbm_batch.m
M       compile.m

Corrected filenames in cg_vbm_batch.m.

------------------------------------------------------------------------
r483 | dahnke | 2013-04-23 15:23:35 +0200 (Tue, 23 Apr 2013) | 10 lines

Changed paths:
M       cg_vbm_write.m
M       vbm_vol_partvol.m
M       vbm_vol_resize.m

(1) Minor changes and corrections for variable names.
(2) Updates for VBM12i skull stripping to get more brain tissue.
(3) Correct BVC error in the non-adaptive pipeline.
(4) Correct resizing error in vbm_vol_partvol for highres images.

------------------------------------------------------------------------
r482 | gaser | 2013-04-23 11:24:11 +0200 (Tue, 23 Apr 2013) | 6 lines

Changed paths:
M       cg_vbm_batch.sh

cg_vbm_batch.sh now allows to define folder for log-files and uses hostname
for log-file.

------------------------------------------------------------------------
r481 | dahnke | 2013-04-23 09:58:25 +0200 (Tue, 23 Apr 2013) | 8 lines

Changed paths:
M       cg_vbm_write.m
M       tbx_cfg_vbm.m
M       vbm_vol_t1qacalc.m

(1) Minor changes and corrections for variable names.
(2) Updates for VBM12i skull stripping to get more brain tissue.

------------------------------------------------------------------------
r480 | dahnke | 2013-04-22 18:17:09 +0200 (Mon, 22 Apr 2013) | 18 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_write.m
A       findfiles.m
A       vbm_io_cprintf.m
M       vbm_io_writenii.m
M       vbm_io_xml.m
A       vbm_vol_t1qacalc.m

(1) Added group expectation maps - a difference map between tissue probability
    map and the final label map.
(2) Minor changes and corrections for variable names.
(3) Added quality assurance routines.
(4) Update error messages for vbm_io_xml.
(5) Add vbm_io_cfprintf for colored command line output.
(6) Update final figure output.


------------------------------------------------------------------------
r479 | gaser | 2013-04-22 17:07:28 +0200 (Mon, 22 Apr 2013) | 7 lines

Changed paths:
M       cg_vbm_batch.m
M       cg_vbm_run.m
M       cg_vbm_batch.sh

Updated batch system.

------------------------------------------------------------------------
r478 | gaser | 2013-04-22 13:24:17 +0200 (Mon, 22 Apr 2013) | 5 lines

Changed paths:
M       cg_vbm_write.m

Changed some handling with deformation field in cg_vbm_write.m.

------------------------------------------------------------------------
r477 | gaser | 2013-04-22 11:08:41 +0200 (Mon, 22 Apr 2013) | 11 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_batch.m
M       cg_vbm_get_defaults.m
M       cg_vbm_write.m

(1) Updated batch call from command line.
(2) Re-added missing mgT and mlT flags to cg_vbm_defaults.m
(3) Changed call job.extopts.BVC to cg_vbm_get_defaults('extopts.BVC')
    in cg_vbm_write.m

------------------------------------------------------------------------
r476 | dahnke | 2013-04-19 17:18:14 +0200 (Fri, 19 Apr 2013) | 25 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       vbm12.txt
MM      vbm_vol_partvol.m
M       vbm_vol_simgrow.c
M       vbm_vol_simgrow.mexmaci64

(1) vbm_vol_partvol:
    Corrected BVC for subjects with thin WM structures (IXI175,OASIS0031).
    Full head-labeling after resizing.
    Add correction for unsafe atlas regions (Hippocampus).
    Corrected CSF in subcortical ROI.
(2) Removed prefix detection in vbm_io_writenii.
(3) Corrected extopts fields for BVC and pbt in cg_vbm_defaults.
(4) Update of the skull stipping of VMB12i.
(5) The only intensity corrected output images (m*.nii) is now the bias and
    noise corrected and intensity normalized images. The locally normalized
    version is only available for internal operations like the thickness
    estimation.
(6) vbm_vol_t1qacalc:
    Preprocessing based quality assurance of T1 images. Write image and subject
    properties to a QA structure with the original measurements and school marks
    rating that based on our experience.

------------------------------------------------------------------------
r475 | gaser | 2013-04-19 10:32:39 +0200 (Fri, 19 Apr 2013) | 6 lines

Changed paths:
M       Makefile.vbm
M       cg_check_cov.m

Some minor changes in cg_check_ocv.m.

------------------------------------------------------------------------
r474 | dahnke | 2013-04-17 18:21:18 +0200 (Wed, 17 Apr 2013) | 5 lines

Changed paths:
M       cg_vbm_write.m

(1) Add a missing variable.

------------------------------------------------------------------------
r473 | dahnke | 2013-04-17 18:12:39 +0200 (Wed, 17 Apr 2013) | 15 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_vbm_write.m
D       vbm_io_niiwrite.m
A  +    vbm_io_writenii.m
M       vbm_vol_partvol.m
M       vbm_vol_pbt.m
M       vbm_vol_resize.m

(1) Added interpolation and deinterpolation function in vbm_vol_resize for
    thickness/surface estimation.
(2) Added blood vessel correction.
(3) Correct error in pcT.


------------------------------------------------------------------------
r472 | dahnke | 2013-04-16 14:44:17 +0200 (Tue, 16 Apr 2013) | 10 lines

Changed paths:
M       cg_vbm_write.m
M       vbm_io_niiwrite.m
D       vbm_pre_partvol.m
A       vbm_vol_partvol.m

(1) Update partitioning for Dartel input and remove old normalization code.
(2) Update blood vessel correction in the partitioning routine.


------------------------------------------------------------------------
r471 | gaser | 2013-04-16 14:31:49 +0200 (Tue, 16 Apr 2013) | 15 lines

Changed paths:
M       vbm_vol_iscale.m
M       cg_vbm_batch.m
 M      templates_1.50mm/l1A.nii
 M      templates_1.50mm/p0A.nii
M       cg_vbm_run.m
M       vbm_io_niiwrite.m
M       cg_slice_overlay.m
M       cg_vbm_write.m

(1) Changed regularization default to new default of SPM12 r5373.
(2) Always use .nii as extension in vbm_io_niiwrite.m.
(3) Replaced fileparts by spm_fileparts.


------------------------------------------------------------------------
r470 | gaser | 2013-04-16 13:54:05 +0200 (Tue, 16 Apr 2013) | 7 lines

Changed paths:
M       cg_vbm_defaults.m
M       vbm12.man

Changed regularization default to new default of SPM12 r5373.


------------------------------------------------------------------------
r469 | dahnke | 2013-04-15 16:51:10 +0200 (Mon, 15 Apr 2013) | 17 lines

Changed paths:
 M      .
M       cg_vbm_write.m
A       templates_1.50mm/l1A.nii
A       templates_1.50mm/p0A.nii
A       vbm_io_niiwrite.m
M       vbm_pre_partvol.m
A       vbm_vol_median3c.c
A       vbm_vol_median3c.mexmaci64
D       vbm_vol_write_nii.m

This update include a lot of new methods and function mostly with alpa-status.
(1) Corrections of vbm_vol_write_nii and renaming to vbm_io_niiwrite
(2) Updates partitioning map (l1*).
(3) Adding of atlas map for major regions for l1* map.
    Runs with default SPM segmentation.

------------------------------------------------------------------------
r468 | gaser | 2013-04-15 15:52:32 +0200 (Mon, 15 Apr 2013) | 26 lines

Changed paths:
D       ornlmMex.mexmaci
D       ornlmMex.mexw64
D       upfirdn2dMex.mexw64
D       farras.m
D       ornlmMex.c
D       ornlmMex.m
D       ornlmMex.mexmaci64
D       ornlmMex.mexglx
D       upfirdn2dMex.mexglx
D       cg_ornlm.m
D       upfirdn2dMex.c
D       upfirdn2dMex.m
D       upfirdn2dMex.mexmaci64
D       ornlmMex.mexa64
D       upfirdn2dMex.mexa64
D       afb3D.m
D       dwt3D.m
D       cg_check_sample_sd.m
D       ornlm.c
D       ornlmMex.mexw32
D       upfirdn2dMex.mexw32
D       upfirdn2dMex.mexmaci

Removed many functions that are not needed anymore.

------------------------------------------------------------------------
r467 | gaser | 2013-04-15 15:41:40 +0200 (Mon, 15 Apr 2013) | 6 lines

Changed paths:
M       cg_vbm_run.m
M       vbm12.man

Hide warning in cg_vbm_run.m that calls spm_affreg.m.

------------------------------------------------------------------------
r466 | gaser | 2013-04-15 14:55:56 +0200 (Mon, 15 Apr 2013) | 23 lines

Changed paths:
D       AmapMexNu.m
M       Makefile.vbm
D       down_cut.mexw64
D       PveAmap_ui.m
D       stat_thresh.m
D       down_cut.mexmaci
D       down_cut.mexglx
D       Pve5Mex.c
D       Pve5Mex.m
D       PveAmap.c
D       PveAmap.h
D       down_cut.mexa64
D       down_cut.c
D       down_cut.mexmaci64
D       KmeansProper.c
D       down_cut.mexw32
D       PveAmapMex.c
D       PveAmapMex.m
D       AmapMexNu.c

Deleted som functions that are not necessary anymore.

------------------------------------------------------------------------
r465 | gaser | 2013-04-15 12:39:36 +0200 (Mon, 15 Apr 2013) | 5 lines

Changed paths:
M       tbx_cfg_vbm.m

Corrected typo in tbx_cfg_vbm.m.

------------------------------------------------------------------------
r464 | gaser | 2013-04-15 12:26:59 +0200 (Mon, 15 Apr 2013) | 5 lines

Changed paths:
M       checkinopt.m

Some editing in checkinopt.m.

------------------------------------------------------------------------
r463 | gaser | 2013-04-15 12:25:27 +0200 (Mon, 15 Apr 2013) | 10 lines

Changed paths:
 M      vbm_stat_nanstat1d.m
 M      vbm_io_handle_pre.m
 M      vbm_vol_simgrow.c
 M      vbm_vol_simgrow.mexmaci64
M       vbm12.txt
 M      vbm_pre_partvol.m

Some editing and reordering in vbm12.txt.

------------------------------------------------------------------------
r462 | gaser | 2013-04-15 12:20:36 +0200 (Mon, 15 Apr 2013) | 5 lines

Changed paths:
M       cg_vbm_defaults.m

Some editing and reordering in cg_vbm_defaults.

------------------------------------------------------------------------
r461 | dahnke | 2013-04-15 10:40:03 +0200 (Mon, 15 Apr 2013) | 77 lines

Changed paths:
M       CHANGES.txt
D       GBM.m
M       cg_vbm_defaults.m
M       cg_vbm_write.m
M       checkinopt.m
M       compile.m
A       ds.m
D       eikonal3.c
D       eikonal3.mexa64
D       eikonal3.mexglx
D       eikonal3.mexmaci
D       eikonal3.mexmaci64
D       eikonal3.mexw32
D       eikonal3.mexw64
M       tbx_cfg_vbm.m
A       templates_1.50mm
M       vbm12.txt
A       vbm_io_handle_pre.m
 M      vbm_io_updateStruct.m
MM      vbm_io_xml.m
A       vbm_pre_partvol.m
A       vbm_stat_nanstat1d.m
A  +    vbm_vol_GBM.m
A       vbm_vol_approx.m
A       vbm_vol_downcut.c
A       vbm_vol_downcut.mexmaci64
A       vbm_vol_eidist.cpp
A       vbm_vol_eidist.mexmaci64
A       vbm_vol_eikonal3.c
A       vbm_vol_eikonal3.mexmaci64
A       vbm_vol_gradient3.c
A       vbm_vol_gradient3.mexmaci64
A       vbm_vol_interp3f.cpp
A       vbm_vol_interp3f.mexmaci64
A       vbm_vol_iscale.m
A       vbm_vol_laplace3.c
A       vbm_vol_laplace3.mexmaci64
A       vbm_vol_laplace3R.c
A       vbm_vol_laplace3R.mexmaci64
MM      vbm_vol_localstat.c
 M      vbm_vol_localstat.mexmaci64
MM      vbm_vol_median3.c
 M      vbm_vol_median3.mexmaci64
A       vbm_vol_morph.m
A       vbm_vol_nanmean3.m
A       vbm_vol_pbt.m
A       vbm_vol_pbtp.cpp
A       vbm_vol_pbtp.mexmaci64
A       vbm_vol_resize.m
A       vbm_vol_simgrow.c
A       vbm_vol_simgrow.mexmaci64
A       vbm_vol_smooth3X.m
A       vbm_vol_write_nii.m

This update include a lot of new methods and function mostly with alpa-status.
(1) Added a global intensity normalisation (mg*.nii) with WM=1, GM=2/3, CSF=1/3.
(2) Added a new local adaptive segmentation (LAD) pipeline with local corrected,
    brain masked version (ml*.nii) of the T1 input with WM=1, GM=2/3, CSF=1/3.
    The new pipeline include:
    - local adaptive tissue peak estimation for lower area PVE especially in
      deep GM structures
    - local sharpening for thin gyral WM structures
    - new final skull-stripping
    - (blood vessel correction)
(3) Added GM thickness estimation (th1*.nii) for RAW-resolution that still
    requires the interpolation for full quality.
(4) Prepare segmentation for major brain regions and sides (l1*.nii).
(5) Added a preprocessing change map to map changes in the preprocessing to
    identify problematic data and processing.
(6) Added XML import/export/update function for MATLAB structures. Replace text
    by XML export (*_seg8.txt > vbm_*.xml).
(7) Added the "vbm_*_" prefix for some function.
(8) Starts replacement of cg_morph_vol by vbm_vol_morph.
(9) Preparing a write function to write a image in different spaces.
(10) Update of the GUI and variables for the additional functions.

------------------------------------------------------------------------
r460 | dahnke | 2013-04-12 10:54:14 +0200 (Fri, 12 Apr 2013) | 1 line

Rename and update of the median filter (median3 > vbm_io_median3).
------------------------------------------------------------------------
r459 | dahnke | 2013-04-12 10:48:55 +0200 (Fri, 12 Apr 2013) | 1 line

Local statistic (mean,min,max,std(,peak)) function for a masked region.
------------------------------------------------------------------------
r458 | dahnke | 2013-04-12 10:47:18 +0200 (Fri, 12 Apr 2013) | 1 line

XML import and export of a MATLAB structure. The main functions based on the xml_io_tools of Jaroslaw Tuszynski from MATLAB Central (Version: 2010-11-05). The vbm_io_xml used the vbm_io_updateStruct function to allow updates of existing files, where parts of the main structure, where replaced by the new input.
------------------------------------------------------------------------
r457 | gaser | 2013-03-28 12:45:37 +0100 (Thu, 28 Mar 2013) | 6 lines

Changed paths:
M       cg_vbm_defaults.m

Use old bounding box, because change of it and voxel size does not yer work
with Dartel.

------------------------------------------------------------------------
r456 | gaser | 2013-03-28 10:49:51 +0100 (Thu, 28 Mar 2013) | 6 lines

Changed paths:
M       cg_vbm_run.m

Removed debugging output in cg_vbm_run.m.


------------------------------------------------------------------------
r455 | gaser | 2013-03-28 10:30:11 +0100 (Thu, 28 Mar 2013) | 6 lines

Changed paths:
M       cg_vbm_run.m

(1) Corrected wromg fwhm value in cg_vbm_run.m.
(2) Removed unnecessary code cg_vbm_run.m.

------------------------------------------------------------------------
r454 | gaser | 2013-03-28 09:19:03 +0100 (Thu, 28 Mar 2013) | 11 lines

Changed paths:
M       cg_vbm_defaults.m
M       tbx_cfg_vbm.m
 M      vbm12.man
M       cg_vbm_write.m

(1) Use now defaults from spm12.
(2) Corrected saving of native bias corrected image.
(3) Removed some changes from last release.


------------------------------------------------------------------------
r453 | dahnke | 2013-03-27 11:05:32 +0100 (Wed, 27 Mar 2013) | 1 line

Little changes for Skull-Stripping and adding of export for the bias and noise corrected image (can find the original part... )
------------------------------------------------------------------------
r452 | gaser | 2013-03-26 15:09:46 +0100 (Tue, 26 Mar 2013) | 13 lines

Changed paths:
M       Makefile.vbm
M       cg_vbm_defaults.m
M       cg_cleanup_gwc.m
M       cg_vbm_tools.m
M       vbm12.txt
M       cg_vbm_write.m

(1) Updated installation folder in Makefile.vbm.
(2) Corrected template folder in cg_vbm_defaults.m.
(3) Corrected typo in cg_cleanup_gwc.m.
(4) Name of volume files is now *seg.txt.

------------------------------------------------------------------------
r451 | gaser | 2013-03-26 14:38:49 +0100 (Tue, 26 Mar 2013) | 24 lines

Changed paths:
M       cg_vbm_defaults.m
M       cg_spm_batch.sh
M       median3.mexa64
M       AmapMex.mexa64
M       eikonal3.mexa64
M       vbdist.mexa64
M       cg_spm_batch.m
M       tbx_cfg_vbm.m
M       cg_vbm_run.m
M       down_cut.mexa64
 M      vbm12.txt
M       CHANGES.txt
M       spm_vbm12.m
M       cg_sanlm.m
A       vbm12.man
M       sanlmMex_noopenmp.mexa64
M       cg_cfg_realign.m
M       sanlmMex.mexa64
M       cg_vbm_write.m

Numerous changes to use spm12 segmentation as starting label. Kmeans is now
deselected by default.

------------------------------------------------------------------------
r450 | gaser | 2013-03-26 14:10:21 +0100 (Tue, 26 Mar 2013) | 6 lines

Changed paths:
M       cg_cleanup_gwc.m
M       CHANGES.txt

Added check whether clustering failed in cg_cleanup_gwc.m.

------------------------------------------------------------------------
r449 | gaser | 2012-09-13 12:53:51 +0200 (Thu, 13 Sep 2012) | 5 lines

Changed paths:
M       tbx_cfg_vbm.m

Corrected "BlaBlaBla" in tbx_cfg_vbm.m

------------------------------------------------------------------------
r448 | dahnke | 2012-07-18 12:33:30 +0200 (Wed, 18 Jul 2012) | 1 line

directory for templates, test and validiation images
------------------------------------------------------------------------
r447 | gaser | 2012-07-18 10:36:17 +0200 (Wed, 18 Jul 2012) | 7 lines

Changed paths:
M       Makefile.vbm
D       spm_vbm.m
A  +    spm_vbm12.m

Renamed spm_vbm.m to spm_vbm12.m to enable toolbox call.

------------------------------------------------------------------------
r446 | gaser | 2012-07-18 10:21:40 +0200 (Wed, 18 Jul 2012) | 5 lines

Changed paths:
M       Makefile.vbm

Changed filenames in Makefile.vbm.

------------------------------------------------------------------------
r445 | gaser | 2012-07-18 09:32:03 +0200 (Wed, 18 Jul 2012) | 10 lines

Changed paths:
A  +    cg_spm_batch.sh
D       test_vbm.m
A  +    cg_spm_batch.m
D       cg_spm8_batch.sh
M       CHANGES.txt
D       cg_spm8_batch.m

Removed some old files and renamed spm8 to spm in filenames.

------------------------------------------------------------------------
r444 | gaser | 2012-07-18 09:28:11 +0200 (Wed, 18 Jul 2012) | 52 lines

Changed paths:
D       cg_vbm12_get_defaults.m
M       Contents_info.txt
A  +    cg_vbm_defs.m
M       Makefile.vbm
D       cg_vbm12_batch.sh
A  +    cg_vbm_defaults.m
A  +    test_vbm.m
D       cg_vbm12_brainmask_ui.m
D       cg_vbm12_defaults.m
A  +    cg_vbm_batch.m
A  +    cg_vbm_update.m
D       cg_vbm12_batch.m
A  +    cg_vbm_tools.m
A  +    cg_vbm_bias_run.m
D       cg_vbm12_tools.m
A  +    tbx_cfg_vbm.m
D       cg_vbm12_longitudinal_multi.m
A  +    cg_vbm_get_defaults.m
D       cg_vbm12_brainmask.m
M       cg_realign.m
A  +    spm_vbm.m
A  +    cg_vbm_longitudinal_multi_run.m
M       cg_spm8_batch.sh
A  +    cg_vbm_longitudinal_multi.m
A  +    cg_vbm_run.m
D       cg_vbm12_bias_run.m
D       test_vbm12.m
D       cg_vbm12_bias.m
D       cg_vbm12_longitudinal.m
R       vbm12.txt
A  +    cg_vbm_brainmask_ui.m
D       cg_vbm12_defs.m
M       cg_spm8_batch.m
D       cg_vbm12_update.m
D       spm_vbm12.m
A  +    cg_vbm_batch.sh
M       cg_sanlm.m
D       cg_vbm12_run.m
A  +    cg_vbm_debug.m
D       cg_vbm12_debug.m
D       cg_vbm12_longitudinal_multi_run.m
M       cg_cfg_realign.m
D       tbx_cfg_vbm12.m
A  +    cg_vbm_brainmask.m
A  +    cg_vbm_bias.m
A  +    cg_vbm_longitudinal.m
A  +    cg_vbm_write.m
D       cg_vbm12_write.m

Changed my mind and renamed all *vbm12* files to *vbm*.

------------------------------------------------------------------------
r443 | gaser | 2012-07-18 09:10:56 +0200 (Wed, 18 Jul 2012) | 27 lines

Changed paths:
M       cg_vbm12_get_defaults.m
M       cg_vbm12_batch.sh
M       cg_vbm12_brainmask_ui.m
M       cg_vbm12_defaults.m
M       cg_vbm12_batch.m
M       cg_vbm12_tools.m
M       cg_vbm12_longitudinal_multi.m
M       cg_vbm12_brainmask.m
M       cg_vbm12_bias_run.m
M       test_vbm12.m
M       cg_vbm12_bias.m
M       cg_vbm12_longitudinal.m
M       cg_vbm12_defs.m
M       cg_vbm12_update.m
M       spm_vbm12.m
M       cg_vbm12_run.m
D       a64
D       a64/libEBTKS.a
M       cg_vbm12_debug.m
M       cg_vbm12_longitudinal_multi_run.m
M       tbx_cfg_vbm12.m
M       cg_vbm12_write.m
M       VBM12-Manual.doc

Renamed all occurances of vbm8 to vbm12.

------------------------------------------------------------------------
r442 | gaser | 2012-07-18 09:09:18 +0200 (Wed, 18 Jul 2012) | 54 lines

Changed paths:
D       cg_vbm8_defs.m
A  +    cg_vbm12_get_defaults.m
D       cg_vbm8_defaults.m
A  +    cg_vbm12_batch.sh
D       spm_vbm8.m
D       vbm8.txt
A  +    cg_vbm12_brainmask_ui.m
D       cg_vbm8_batch.m
D       cg_vbm8_update.m
A  +    cg_vbm12_defaults.m
A  +    cg_vbm12_batch.m
D       cg_vbm8_tools.m
D       VBM8-Manual_Japanese.doc
D       cg_vbm8_bias_run.m
D       cg_vbm8_get_defaults.m
A  +    cg_vbm12_tools.m
A  +    cg_vbm12_longitudinal_multi.m
A  +    VBM12-Manual_Japanese.pdf
A  +    cg_vbm12_brainmask.m
D       cg_vbm8_longitudinal_multi_run.m
D       cg_vbm8_longitudinal_multi.m
D       cg_vbm8_run.m
A  +    cg_vbm12_bias_run.m
A  +    test_vbm12.m
A  +    cg_vbm12_bias.m
D       VBM8-Manual.pdf
A  +    cg_vbm12_longitudinal.m
D       cg_vbm8_brainmask_ui.m
A  +    vbm12.txt
A  +    VBM12-Manual.pdf
A  +    cg_vbm12_defs.m
A  +    cg_vbm12_update.m
D       cg_vbm8_batch.sh
A  +    spm_vbm12.m
D       tbx_cfg_vbm8.m
A  +    VBM12-Manual_Japanese.doc
A  +    cg_vbm12_run.m
D       cg_vbm8_debug.m
A  +    cg_vbm12_debug.m
A  +    cg_vbm12_longitudinal_multi_run.m
D       cg_vbm8_brainmask.m
D       cg_vbm8_bias.m
A  +    tbx_cfg_vbm12.m
D       cg_vbm8_longitudinal.m
D       cg_vbm8_write.m
D       VBM8-Manual.doc
D       VBM8-Manual_Japanese.pdf
A  +    cg_vbm12_write.m
D       test_vbm8.m
A  +    VBM12-Manual.doc

Renamed all files from vbm8 to vbm12.

------------------------------------------------------------------------
r441 | gaser | 2012-07-18 09:03:10 +0200 (Wed, 18 Jul 2012) | 38 lines

Changed paths:
!       cg_vbm8_defs.m
M       Contents_info.txt
M       Makefile.vbm
!       cg_vbm8_defaults.m
!       spm_vbm8.m
!       vbm8.txt
!       cg_vbm8_batch.m
!       cg_vbm8_update.m
!       cg_vbm8_tools.m
!       VBM8-Manual_Japanese.doc
!       cg_vbm8_bias_run.m
M       Anatomy2Dartel.txt
!       cg_vbm8_get_defaults.m
M       cg_realign.m
!       cg_vbm8_longitudinal_multi_run.m
!       cg_vbm8_longitudinal_multi.m
!       cg_vbm8_run.m
!       VBM8-Manual.pdf
!       cg_vbm8_brainmask_ui.m
M       CHANGES.txt
M       cg_spm8_batch.m
!       cg_vbm8_batch.sh
M       INSTALL_info.txt
!       tbx_cfg_vbm8.m
M       cg_sanlm.m
!       cg_vbm8_debug.m
M       cg_cfg_realign.m
!       cg_vbm8_brainmask.m
!       cg_vbm8_bias.m
!       cg_vbm8_longitudinal.m
!       cg_vbm8_write.m
!       VBM8-Manual.doc
!       VBM8-Manual_Japanese.pdf
!       test_vbm8.m

Renamed all occurance of vbm8 to vbm12.

------------------------------------------------------------------------
r440 | gaser | 2012-03-28 09:50:58 +0200 (Wed, 28 Mar 2012) | 7 lines

Changed paths:
M       cg_vbm8_defs.m
M       cg_ornlm.m
M       CHANGES.txt

Added HDW path to cg_vbm8_defs.m.

------------------------------------------------------------------------
